/devtools/trunk

To get this branch, use:
bzr branch /scm/loggerhead/devtools/trunk
1 by Marcin Wojdyr
initial revision of jhbuild config
1
<?xml version="1.0"?><!--*- mode: nxml; indent-tabs-mode: nil -*-->
2
<!DOCTYPE moduleset SYSTEM "moduleset.dtd">
3
<?xml-stylesheet type="text/xsl" href="moduleset.xsl"?>
4
<!--
5
     Syntax reference:
6
     http://developer.gnome.org/jhbuild/unstable/moduleset-syntax.html.en
7
 -->
8
<moduleset>
62 by Marcin Wojdyr
updated ccp4-jhbuild
9
  <repository type="bzr" name="oisin" default="yes"
1340 by Charles Ballard
looks like http is faster than bzr+http
10
              href="http://fg.oisin.rc-harwell.ac.uk/bzr/"
294 by Marcin Wojdyr
adjust bundle-sources script to bundle branch 5.8 of refmac
11
              trunk-template="%(module)s/trunk/"
12
              branches-template="%(module)s/%(branch)s/"/>
1 by Marcin Wojdyr
initial revision of jhbuild config
13
  <repository type="tarball" name="ccp4-tarballs"
7 by Marcin Wojdyr
added refmac
14
              href="ftp://ftp.ccp4.ac.uk/opensource/"/>
136 by Marcin Wojdyr
updates
15
  <repository type="tarball" name="files"
132 by Marcin Wojdyr
updated moduleset
16
              href="http://devtools.fg.oisin.rc-harwell.ac.uk/files/"/>
306 by Marcin Wojdyr
added more coot dependencies
17
  <repository type="tarball" name="sf"
18
              href="http://downloads.sourceforge.net/"/>
1076 by Marcin Wojdyr
added probe and reduce from github.com/rlabduke
19
  <repository type="tarball" name="github-zip" href="https://github.com/"/>
1178 by Marcin Wojdyr
take dimple from github.com/ccp4/dimple
20
  <repository type="git" name="github" href="https://github.com/"/>
1332 by Charles Ballard
move of ccpem to gitlab
21
  <repository type="git" name="gitlab" href="https://gitlab.com/"/>
71 by Marcin Wojdyr
added cmake to the modules
22
957 by Marcin Wojdyr
updates for ccp4-core -> ccp4-base, ... transition
23
  <custom id="ccp4-base" install_to="* ./">
24
    <branch/>
25
  </custom>
26
1 by Marcin Wojdyr
initial revision of jhbuild config
27
  <autotools id="mmdb">
62 by Marcin Wojdyr
updated ccp4-jhbuild
28
    <branch/>
1 by Marcin Wojdyr
initial revision of jhbuild config
29
  </autotools>
30
673 by Marcin Wojdyr
ccp4.xml: added mmdb2
31
  <autotools id="mmdb2">
32
    <branch/>
33
  </autotools>
34
388 by Marcin Wojdyr
ccp4.xml: add --datadir=${prefix}/lib/data to libccp4
35
  <autotools id="libccp4" autogenargs="--datadir=${prefix}/lib/data">
36
    <branch/>
37
    <dependencies>
957 by Marcin Wojdyr
updates for ccp4-core -> ccp4-base, ... transition
38
      <dep package="ccp4-base"/>
868 by Marcin Wojdyr
libccp4 is linked now with mmdb2
39
      <dep package="mmdb2"/>
388 by Marcin Wojdyr
ccp4.xml: add --datadir=${prefix}/lib/data to libccp4
40
    </dependencies>
41
  </autotools>
42
183 by Marcin Wojdyr
minor updated here and there
43
  <autotools id="ccif" autogenargs="--with-ccp4">
168 by Marcin Wojdyr
a few updates to the moduleset
44
    <branch/>
183 by Marcin Wojdyr
minor updated here and there
45
    <dependencies>
46
      <dep package="libccp4"/>
47
    </dependencies>
492 by Marcin Wojdyr
ccp4.xml: changes in libgnurx
48
    <after>
49
      <dep package="libgnurx"/> <!-- may be needed on Windows only -->
50
    </after>
1 by Marcin Wojdyr
initial revision of jhbuild config
51
  </autotools>
52
46 by Marcin Wojdyr
added gesamt to build script
53
  <autotools id="ssm" autogenargs="--enable-ccp4">
62 by Marcin Wojdyr
updated ccp4-jhbuild
54
    <branch/>
1 by Marcin Wojdyr
initial revision of jhbuild config
55
    <dependencies>
678 by Marcin Wojdyr
ccp4.xml: add mmdb2 as (future) dependency for ssm, pisa, etc
56
      <dep package="mmdb2"/>
1 by Marcin Wojdyr
initial revision of jhbuild config
57
      <dep package="libccp4"/>
58
    </dependencies>
59
  </autotools>
60
691 by Marcin Wojdyr
ccp4.xml: gesamt using now cmake and mmdb2
61
  <cmake id="gesamt" cmakeargs="-DUSE_CCP4=1">
62 by Marcin Wojdyr
updated ccp4-jhbuild
62
    <branch/>
46 by Marcin Wojdyr
added gesamt to build script
63
    <dependencies>
678 by Marcin Wojdyr
ccp4.xml: add mmdb2 as (future) dependency for ssm, pisa, etc
64
      <dep package="mmdb2"/>
46 by Marcin Wojdyr
added gesamt to build script
65
      <dep package="libccp4"/>
1242 by Marcin Wojdyr
gesamt now depends on jsrview
66
      <dep package="jsrview"/>
46 by Marcin Wojdyr
added gesamt to build script
67
    </dependencies>
691 by Marcin Wojdyr
ccp4.xml: gesamt using now cmake and mmdb2
68
  </cmake>
46 by Marcin Wojdyr
added gesamt to build script
69
1 by Marcin Wojdyr
initial revision of jhbuild config
70
  <autotools id="ccp4srs">
62 by Marcin Wojdyr
updated ccp4-jhbuild
71
    <branch/>
1 by Marcin Wojdyr
initial revision of jhbuild config
72
    <dependencies>
678 by Marcin Wojdyr
ccp4.xml: add mmdb2 as (future) dependency for ssm, pisa, etc
73
      <dep package="mmdb2"/>
137 by Marcin Wojdyr
ccp4srs now depends on zlib
74
      <dep package="zlib"/>
232 by Marcin Wojdyr
disable parallel building (make -jN) of FFTW2, it sometimes goes wrong
75
      <dep package="ccp4srs-data"/>
1 by Marcin Wojdyr
initial revision of jhbuild config
76
    </dependencies>
77
  </autotools>
78
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
79
  <custom id="ccp4srs-data"
263 by Marcin Wojdyr
use xia2 from svn (again), avoid copying .bzr/.svn dirs on install
80
          install_to="* share/ccp4srs/">
1042 by Marcin Wojdyr
update ccp4srs-data
81
    <branch repo="ccp4-tarballs" version="20150205"
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
82
            module="ccp4srs-data-${version}.tar.gz"/>
83
  </custom>
84
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
85
  <cmake id="qtlibs">
86
    <branch/>
87
    <dependencies>
88
    </dependencies>
89
  </cmake>
90
297 by Marcin Wojdyr
moduleset: added pseudo-module pisa-no-qt
91
  <!-- special case, building pisa without qtpisa -->
92
  <cmake id="pisa-no-qt" cmakeargs="-DUSE_QT=OFF">
93
    <branch module="pisa"/>
94
    <dependencies>
678 by Marcin Wojdyr
ccp4.xml: add mmdb2 as (future) dependency for ssm, pisa, etc
95
      <dep package="mmdb2"/>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
96
      <dep package="ssm"/>
297 by Marcin Wojdyr
moduleset: added pseudo-module pisa-no-qt
97
      <dep package="libccp4"/>
98
      <dep package="ccp4srs"/>
99
      <dep package="ccp4srs-data"/>
100
    </dependencies>
101
  </cmake>
102
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
103
  <cmake id="pisa">
62 by Marcin Wojdyr
updated ccp4-jhbuild
104
    <branch/>
6 by Marcin Wojdyr
added pisa
105
    <dependencies>
678 by Marcin Wojdyr
ccp4.xml: add mmdb2 as (future) dependency for ssm, pisa, etc
106
      <dep package="mmdb2"/>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
107
      <dep package="ssm"/>
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
108
      <dep package="libccp4"/>
6 by Marcin Wojdyr
added pisa
109
      <dep package="ccp4srs"/>
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
110
      <dep package="ccp4srs-data"/>
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
111
      <dep package="qtlibs"/>
6 by Marcin Wojdyr
added pisa
112
    </dependencies>
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
113
  </cmake>
6 by Marcin Wojdyr
added pisa
114
115
  <cmake id="refmac">
290 by Marcin Wojdyr
refmac: change directory name to refmac5.8 to avoid conflicts on update
116
    <branch branch="5.8" checkoutdir="refmac5.8"/>
7 by Marcin Wojdyr
added refmac
117
    <dependencies>
118
      <dep package="libccp4"/>
119
      <dep package="lapack"/>
886 by Marcin Wojdyr
ccp4.xml: refmac now requires FFTW2
120
      <dep package="fftw2"/>
7 by Marcin Wojdyr
added refmac
121
    </dependencies>
6 by Marcin Wojdyr
added pisa
122
  </cmake>
123
190 by Marcin Wojdyr
moduleset changes: new LAPACK, refmac_dictionary is now in bazaar
124
  <custom id="monomers"
263 by Marcin Wojdyr
use xia2 from svn (again), avoid copying .bzr/.svn dirs on install
125
      install_to="* lib/data/monomers/">
190 by Marcin Wojdyr
moduleset changes: new LAPACK, refmac_dictionary is now in bazaar
126
    <branch/>
127
    <!--
183 by Marcin Wojdyr
minor updated here and there
128
    <branch repo="refmac_experimental" version="5.38"
150 by Marcin Wojdyr
misc changes
129
            module="refmac_dictionary_v${version}.tar.gz"
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
130
            checkoutdir="refmac_dictionary_v${version}"/>
190 by Marcin Wojdyr
moduleset changes: new LAPACK, refmac_dictionary is now in bazaar
131
    -->
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
132
  </custom>
85 by Marcin Wojdyr
added refmac_dictionary to modules
133
15 by Marcin Wojdyr
added ccp4 from CVS (with cmake) to ccp4.modules
134
  <cmake id="ccp4-progs">
219 by Marcin Wojdyr
updated moduleset to add new bzr modules
135
    <branch/>
15 by Marcin Wojdyr
added ccp4 from CVS (with cmake) to ccp4.modules
136
    <dependencies>
137
      <dep package="libccp4"/>
186 by Marcin Wojdyr
ccp4-progs depends on ccif
138
      <dep package="ccif"/>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
139
      <dep package="mmdb2"/>
15 by Marcin Wojdyr
added ccp4 from CVS (with cmake) to ccp4.modules
140
    </dependencies>
141
  </cmake>
142
1284 by Charles Ballard
try to merge in changes from series-71
143
  <cmake id="amore-rs">
144
    <branch/>
145
    <dependencies>
146
      <dep package="libccp4"/>
1331 by Charles Ballard
ccif dependency for amore-rs stub
147
      <dep package="ccif"/>
1284 by Charles Ballard
try to merge in changes from series-71
148
      <dep package="mmdb2"/>
149
    </dependencies>
150
  </cmake>
151
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
152
  <custom id="examples"
263 by Marcin Wojdyr
use xia2 from svn (again), avoid copying .bzr/.svn dirs on install
153
          install_to="* examples/">
314 by Marcin Wojdyr
use bzr checkout --light for mrbump, examples and ccp4-core
154
    <branch light="yes"/> <!-- whole repo is big, 280MB -->
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
155
  </custom>
147 by Marcin Wojdyr
misc updates
156
177 by Marcin Wojdyr
updated moduleset
157
  <custom id="documentation"
922 by Marcin Wojdyr
use documentation/installer.sh script for installing documentation
158
          install="./installer.sh ${dest}">
177 by Marcin Wojdyr
updated moduleset
159
    <branch/>
160
  </custom>
161
957 by Marcin Wojdyr
updates for ccp4-core -> ccp4-base, ... transition
162
  <custom id="ccp4-lib-data" install_to="* lib/data/">
163
    <branch repo="files" module="ccp4-lib-data-6.5.0.tar.gz"
164
            size="15269420" version="6.5.0"/>
165
  </custom>
166
597 by Marcin Wojdyr
ccp4.xml: added test-sys (download-only)
167
  <custom id="test-sys">
168
    <branch/>
169
  </custom>
170
29 by Marcin Wojdyr
added ccp4i to build script
171
  <cmake id="ccp4i">
168 by Marcin Wojdyr
a few updates to the moduleset
172
    <branch/>
173
  </cmake>
174
263 by Marcin Wojdyr
use xia2 from svn (again), avoid copying .bzr/.svn dirs on install
175
  <custom id="imosflm" install_to="* share/ccp4i/imosflm/">
219 by Marcin Wojdyr
updated moduleset to add new bzr modules
176
    <branch/>
177
  </custom>
178
723 by Marcin Wojdyr
ccp4.xml: added hklfile
179
  <cmake id="hklfile">
180
    <branch/>
907 by Marcin Wojdyr
ccp4.xml: specify deps for hklfile
181
    <dependencies>
182
      <dep package="libccp4"/>
183
      <dep package="clipper"/>
184
    </dependencies>
723 by Marcin Wojdyr
ccp4.xml: added hklfile
185
  </cmake>
186
168 by Marcin Wojdyr
a few updates to the moduleset
187
  <cmake id="viewhkl">
188
    <branch/>
185 by Marcin Wojdyr
moduleset: add viewhkl dependencies
189
    <dependencies>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
190
      <dep package="mmdb2"/>
185 by Marcin Wojdyr
moduleset: add viewhkl dependencies
191
      <dep package="libccp4"/>
192
      <dep package="clipper"/>
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
193
      <dep package="qtlibs"/>
723 by Marcin Wojdyr
ccp4.xml: added hklfile
194
      <dep package="hklfile"/>
185 by Marcin Wojdyr
moduleset: add viewhkl dependencies
195
    </dependencies>
168 by Marcin Wojdyr
a few updates to the moduleset
196
  </cmake>
197
220 by Marcin Wojdyr
added qtrview
198
  <cmake id="qtrview">
199
    <branch/>
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
200
    <dependencies>
201
      <dep package="qtlibs"/>
202
    </dependencies>
220 by Marcin Wojdyr
added qtrview
203
  </cmake>
204
960 by Andrey Lebedev
jsrview build corrected
205
  <cmake id="jsrview">
586 by Marcin Wojdyr
ccp4.xml: added download-only jsrview module
206
    <branch/>
1257.1.25 by Andrey Lebedev
added morda-mp
207
<!--
586 by Marcin Wojdyr
ccp4.xml: added download-only jsrview module
208
    <dependencies>
209
      <dep package="qtlibs"/>
210
    </dependencies>
1257.1.25 by Andrey Lebedev
added morda-mp
211
-->
960 by Andrey Lebedev
jsrview build corrected
212
  </cmake>
586 by Marcin Wojdyr
ccp4.xml: added download-only jsrview module
213
168 by Marcin Wojdyr
a few updates to the moduleset
214
  <cmake id="setup">
215
    <branch/>
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
216
    <dependencies>
217
      <dep package="qtlibs"/>
218
    </dependencies>
168 by Marcin Wojdyr
a few updates to the moduleset
219
  </cmake>
220
1181 by ronan.keegan at ac
updated mrbump installer and update to hmmer location
221
  <cmake id="mrbump">
222
    <branch/>
223
    <dependencies>
224
      <dep package="hmmer"/>
225
      <dep package="mafft"/>
226
      <dep package="clustalw2"/>
227
    </dependencies>
228
  </cmake>
146 by Marcin Wojdyr
updated moduleset
229
247 by Marcin Wojdyr
ccp4.xml: added dssp to to modulset (although not to "all" meta-module yet)
230
  <cmake id="dssp">
231
    <branch/>
679 by Marcin Wojdyr
ccp4.xml & conf.py: build boost with python and cctbx with external boost
232
    <dependencies>
372 by Marcin Wojdyr
ccp4.xml: add boost
233
      <dep package="boost"/>
679 by Marcin Wojdyr
ccp4.xml & conf.py: build boost with python and cctbx with external boost
234
    </dependencies>
247 by Marcin Wojdyr
ccp4.xml: added dssp to to modulset (although not to "all" meta-module yet)
235
  </cmake>
236
1113 by Marcin Wojdyr
added xssp
237
  <cmake id="xssp">
238
    <branch repo="github-zip"
239
        module="cmbi/xssp/releases/download/${version}/xssp-${version}.tar.gz"
240
        version="2.2.7" size="236575">
241
      <patch file="xssp.patch" strip="0" />
242
    </branch>
243
    <dependencies>
244
      <dep package="boost"/>
245
    </dependencies>
246
  </cmake>
247
309 by Marcin Wojdyr
ccp4.xml: added tgutils
248
  <cmake id="tgutils">
249
    <branch/>
377 by Marcin Wojdyr
ccp4.xml: add missing dependency
250
    <dependencies>
251
      <dep package="clipper"/>
252
    </dependencies>
309 by Marcin Wojdyr
ccp4.xml: added tgutils
253
  </cmake>
254
284 by Marcin Wojdyr
moduleset: added dimple to default set of packages
255
  <cmake id="dimple">
1202 by Marcin Wojdyr
on Eugene's request, take dimple from bazaar not from git
256
    <!-- directly from git repo:
1178 by Marcin Wojdyr
take dimple from github.com/ccp4/dimple
257
    <branch repo="github" module="ccp4/dimple.git"/>
1202 by Marcin Wojdyr
on Eugene's request, take dimple from bazaar not from git
258
    or from ccp4 bzr repo: -->
259
    <branch/>
286 by Marcin Wojdyr
moduleset: dimple depends on clipper
260
    <dependencies>
261
      <dep package="clipper"/>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
262
      <dep package="mmdb2"/>
286 by Marcin Wojdyr
moduleset: dimple depends on clipper
263
    </dependencies>
284 by Marcin Wojdyr
moduleset: added dimple to default set of packages
264
  </cmake>
236 by Marcin Wojdyr
moduleset: added ample and dimple
265
1195 by ronan.keegan at ac
AMPLE now cmake and module in python
266
  <cmake id="ample">
1333 by Charles Ballard
ample to github-zip
267
    <branch repo="github-zip"
268
            version="1.3.0"
269
            module="rigdenlab/ample/archive/${version}.zip"
270
            checkoutdir="ample-${version}">
271
    </branch>
1195 by ronan.keegan at ac
AMPLE now cmake and module in python
272
    <dependencies>
1333 by Charles Ballard
ample to github-zip
273
      <dep package="numpy"/>
274
      <dep package="conkit"/>
275
      <dep package="matplotlib"/>
276
      <dep package="biopython"/>
277
      <dep package="pandas"/>
1195 by ronan.keegan at ac
AMPLE now cmake and module in python
278
      <dep package="theseus"/>
279
      <dep package="spicker"/>
1333 by Charles Ballard
ample to github-zip
280
      <dep package="mrbump"/>
1195 by ronan.keegan at ac
AMPLE now cmake and module in python
281
    </dependencies>
282
  </cmake>
236 by Marcin Wojdyr
moduleset: added ample and dimple
283
1269 by Charles Ballard
use autogen.sh -> configure for swig
284
  <autotools id="swig" autogenargs="--bindir=${prefix}/devbin --without-pcre --disable-ccache --without-ocaml"
285
    autogen-sh="configure">
592 by Charles Ballard
add swig for mg build, needed on osx unless have already installed
286
    <branch repo="sf" module="swig/swig-${version}.tar.gz"
1100 by Marcin Wojdyr
update swig 3.0.6 to 3.0.7
287
            version="3.0.7" size="5923046"/>
592 by Charles Ballard
add swig for mg build, needed on osx unless have already installed
288
  </autotools>
289
542 by Marcin Wojdyr
update ccp4mg in ccp4.xml (but it's not working yet)
290
  <cmake id="ccp4mg">
748 by Marcin Wojdyr
ccp4.xml: switch ccp4mg from branch ccp4-jhbuild-distutils to branch ccp4
291
    <branch branch="ccp4"/>
546 by Marcin Wojdyr
some dependencies for ccp4mg
292
    <dependencies>
293
      <dep package="clipper"/>
789 by Marcin Wojdyr
ccp4.xml: add hklfile to MG dependencies
294
      <dep package="hklfile"/>
546 by Marcin Wojdyr
some dependencies for ccp4mg
295
      <dep package="ssm"/>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
296
      <dep package="mmdb2"/>
546 by Marcin Wojdyr
some dependencies for ccp4mg
297
      <dep package="libccp4"/>
1058 by Marcin Wojdyr
ccp4.xml: mg depends on ccp4srs
298
      <dep package="ccp4srs"/>
593 by Charles Ballard
pyqt4 as explicit dependency for ccp4mg
299
      <dep package="pyqt4"/>
1023 by Marcin Wojdyr
modified dependecies: added ccp4mg to "default", pixie and matplotlib to ccp4mg,
300
      <dep package="rdkit"/>
625 by Marcin Wojdyr
ccp4.xml: add suds and lxml as dependencies of MG
301
      <!-- below are runtime dependencies, kind of optional -->
302
      <dep package="suds"/>
303
      <dep package="lxml"/>
1023 by Marcin Wojdyr
modified dependecies: added ccp4mg to "default", pixie and matplotlib to ccp4mg,
304
      <dep package="matplotlib"/>
305
      <dep package="pixie"/>
546 by Marcin Wojdyr
some dependencies for ccp4mg
306
    </dependencies>
542 by Marcin Wojdyr
update ccp4mg in ccp4.xml (but it's not working yet)
307
  </cmake>
242 by Marcin Wojdyr
updated README and ccp4.xml
308
903 by Marcin Wojdyr
ccp4.xml: use cmake for i2
309
  <cmake id="ccp4i2">
867 by Marcin Wojdyr
ccp4.xml & misc/watch-repos.py: add ccp4i2 repo
310
    <branch/>
1284 by Charles Ballard
try to merge in changes from series-71
311
    <dependencies>
312
    <dep package="psutil"/>
313
    </dependencies>
903 by Marcin Wojdyr
ccp4.xml: use cmake for i2
314
  </cmake>
867 by Marcin Wojdyr
ccp4.xml & misc/watch-repos.py: add ccp4i2 repo
315
188 by Marcin Wojdyr
jligand is now in bazaar
316
  <custom id="jligand"
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
317
          build="make" clean="make clean"
277 by Marcin Wojdyr
added hklview and a few other modules
318
          install_to="JLigand.jar bin/, jligand bin/">
188 by Marcin Wojdyr
jligand is now in bazaar
319
    <branch/>
177 by Marcin Wojdyr
updated moduleset
320
  </custom>
99 by Marcin Wojdyr
minor changes in moduleset and in docs
321
168 by Marcin Wojdyr
a few updates to the moduleset
322
  <cmake id="molrep">
323
    <branch/>
324
    <dependencies>
325
      <dep package="libccp4"/>
326
    </dependencies>
327
  </cmake>
328
177 by Marcin Wojdyr
updated moduleset
329
  <cmake id="sfcheck">
330
    <branch/>
331
    <dependencies>
332
      <dep package="libccp4"/>
333
    </dependencies>
334
  </cmake>
335
206 by Marcin Wojdyr
moduleset: build procheck from bazaar
336
  <cmake id="procheck">
337
    <branch/>
338
    <dependencies>
339
      <dep package="libccp4"/>
340
    </dependencies>
341
  </cmake>
342
219 by Marcin Wojdyr
updated moduleset to add new bzr modules
343
  <cmake id="scala">
344
    <branch/>
345
    <dependencies>
346
      <dep package="libccp4"/>
347
      <dep package="lapack"/>
348
    </dependencies>
349
  </cmake>
350
351
  <cmake id="dm21">
352
    <branch/>
353
    <dependencies>
354
      <dep package="libccp4"/>
355
      <dep package="ccif"/>
356
    </dependencies>
357
  </cmake>
358
359
  <cmake id="ccp4-deprecated">
360
    <branch/>
361
    <dependencies>
362
      <dep package="libccp4"/>
363
      <dep package="ccif"/>
364
      <dep package="lapack"/>
365
    </dependencies>
366
  </cmake>
367
890 by Marcin Wojdyr
ccp4.xml: use cmake for edstats, to make things easier
368
  <cmake id="edstats">
279 by Marcin Wojdyr
moduleset: added edstats
369
    <branch/>
283 by Marcin Wojdyr
moduleset: edstats depends on libccp4
370
    <dependencies>
371
      <dep package="libccp4"/>
372
    </dependencies>
890 by Marcin Wojdyr
ccp4.xml: use cmake for edstats, to make things easier
373
  </cmake>
279 by Marcin Wojdyr
moduleset: added edstats
374
537 by Marcin Wojdyr
ccp4.xml: another fix in the same place
375
  <autotools id="mosflm" skip-autogen="never"
376
             autogenargs="--with-ccp4-prefix=${prefix}"
536 by Marcin Wojdyr
fix ccp4.xml
377
             supports-non-srcdir-builds="no" makeargs="-j1 clean all">
535 by Marcin Wojdyr
ccp4.xml: use mosflm from bzr
378
  <branch/>
399 by Marcin Wojdyr
added mosflm
379
    <dependencies>
380
      <dep package="libccp4"/>
381
      <dep package="xdl-view"/>
382
    </dependencies>
383
  </autotools>
384
394 by Marcin Wojdyr
add note about Xt
385
  <!-- requires libxt-dev/libXt-devel -->
277 by Marcin Wojdyr
added hklview and a few other modules
386
  <autotools id="xdl-view" autogen-sh="src/configure">
387
    <branch/>
388
  </autotools>
389
390
  <cmake id="hklview">
391
    <branch/>
392
    <dependencies>
393
      <dep package="libccp4"/>
394
      <dep package="xdl-view"/>
395
    </dependencies>
396
  </cmake>
397
398
  <autotools id="jwc-c">
399
    <branch/>
400
    <dependencies>
401
      <dep package="libccp4"/>
402
    </dependencies>
403
  </autotools>
404
405
  <autotools id="jwc-f">
406
    <dependencies>
407
      <dep package="jwc-c"/>
408
      <dep package="libccp4"/>
409
    </dependencies>
410
    <branch/>
411
  </autotools>
412
1038 by Marcin Wojdyr
build rotgen using cmake
413
  <cmake id="rotgen">
532 by Marcin Wojdyr
ccp4.xml: use rotgen from bzr
414
    <branch/>
398 by Marcin Wojdyr
added rotgen
415
    <dependencies>
416
      <dep package="jwc-f"/>
417
      <dep package="xdl-view"/>
418
    </dependencies>
1038 by Marcin Wojdyr
build rotgen using cmake
419
  </cmake>
398 by Marcin Wojdyr
added rotgen
420
970 by Marcin Wojdyr
ccp4.xml: install README.USAGE from balbes-pipeline
421
  <custom id="balbes-pipeline" install_to="README.USAGE BALBES/, Package/* BALBES/">
969 by Marcin Wojdyr
ccp4.xml: added balbesdb and metamodule balbes
422
    <branch/>
423
  </custom>
424
425
  <custom id="balbesdb" install_to="Package/* BALBES/">
277 by Marcin Wojdyr
added hklview and a few other modules
426
    <branch/>
427
  </custom>
428
429
  <autotools id="dl-laue">
430
    <branch branch="laue/trunk"/>
431
  </autotools>
224 by Marcin Wojdyr
added ccp4-progs to moduleset
432
416 by Marcin Wojdyr
ccp4.xml: install ccp4dispatchers/releaseme/* to libexec/
433
  <custom id="ccp4dispatchers"
434
          install_to="releaseme/* libexec/">
358 by Marcin Wojdyr
small fixes
435
    <branch/>
436
  </custom>
437
365 by Marcin Wojdyr
minor tweaks
438
  <custom id="devtools"> <!-- only for use in bundling script -->
439
    <branch/>
440
  </custom>
441
959 by Marcin Wojdyr
ccp4.xml: coot --without-enhanced-... doesn't work as expected, removed
442
  <cmake id="ccp4-core"> <!-- not used anymore -->
1011 by Marcin Wojdyr
ccp4.xml: rename ccp4-core trunk to old-trunk (to make it clear it's not used)
443
    <branch branch="old-trunk" light="yes"/>
219 by Marcin Wojdyr
updated moduleset to add new bzr modules
444
  </cmake>
445
136 by Marcin Wojdyr
updates
446
  <autotools id="clipper" autogen-sh="configure"
528 by Marcin Wojdyr
ccp4.xml: no need to --enable-fortran in clipper
447
      autogenargs="--enable-ccp4 --enable-mmdb --enable-cif --enable-minimol">
136 by Marcin Wojdyr
updates
448
    <branch/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
449
    <dependencies>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
450
      <dep package="mmdb2"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
451
      <dep package="libccp4"/>
98 by Marcin Wojdyr
updated moduleset
452
      <dep package="fftw2"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
453
    </dependencies>
454
  </autotools>
455
1065 by Marcin Wojdyr
add clipper-python and ccp4srs-python to the build
456
  <cmake id="clipper-python">
457
    <branch branch="trunk"/>
458
    <dependencies>
1334 by Charles Ballard
add lxml dep for clipper python
459
      <dep package="lxml"/>
1065 by Marcin Wojdyr
add clipper-python and ccp4srs-python to the build
460
      <dep package="libccp4"/>
461
      <dep package="clipper"/>
1194 by Marcin Wojdyr
clipper-python depends now on numpy
462
      <dep package="numpy"/>
1065 by Marcin Wojdyr
add clipper-python and ccp4srs-python to the build
463
    </dependencies>
464
  </cmake>
465
466
  <cmake id="ccp4srs-python">
467
    <branch branch="trunk"/>
468
    <dependencies>
469
      <dep package="ccp4srs"/>
470
    </dependencies>
471
  </cmake>
472
211 by Marcin Wojdyr
updated moduleset
473
  <!-- cctbx w/ phaser (phaser can be build only as cctbx subdirectory) -->
368 by Marcin Wojdyr
ccp4.xml: use custom module type for cctbx
474
  <custom id="cctbx-phaser"
475
          configure="sh ${srcdir}/autogen.sh ${prefix} ${libdir}"
476
          build="${}" install="${}" clean="${}"
477
          supports-non-srcdir-builds="yes">
1247 by Charles Ballard
use cctbx version bundled as latest on our site
478
    <branch repo="files" version="latest"
1284 by Charles Ballard
try to merge in changes from series-71
479
            module="cctbx-phaser-dials-molprobity-${version}.tar.gz"
1250 by Charles Ballard
set checkoutdir for cctbx-phaser, back ported from release branches
480
            checkoutdir="cctbx-phaser" >
63 by Marcin Wojdyr
updated ccp4-jhbuild
481
      <patch file="cctbx-autogen.patch" strip="0" />
251 by Marcin Wojdyr
updated cctbx/phaser to current nightly built version
482
      <patch file="cctbx-no-unroll.patch" strip="0" />
255 by Marcin Wojdyr
added patch to cctbx to suppport LDFLAGS env var.
483
      <patch file="cctbx-ldflags.patch" strip="0" />
448 by Marcin Wojdyr
added patch for compilation of cctbx/annlib with MinGW
484
      <patch file="cctbx-ann-mingw.patch" strip="0" />
509 by Charles Ballard
add patches for intel compilers on mac to cctbx
485
      <patch file="cctbx-icc.patch" strip="0" />
679 by Marcin Wojdyr
ccp4.xml & conf.py: build boost with python and cctbx with external boost
486
      <patch file="cctbx-system-boost.patch" strip="0" />
1278 by Charles Ballard
some cctbx-phaser patches
487
      <patch file="cctbx-xia2-nprocs.patch" strip="0" />
488
      <patch file="cctbx-dxtbx-SConscript.patch" strip="0" />
489
      <patch file="phaser-output-toggle.patch" strip="0" />
490
      <patch file="cctbx-cbf-context.patch" strip="0" />
1284 by Charles Ballard
try to merge in changes from series-71
491
      <patch file="cctbx-molprobity.patch" strip="0" />
63 by Marcin Wojdyr
updated ccp4-jhbuild
492
    </branch>
679 by Marcin Wojdyr
ccp4.xml & conf.py: build boost with python and cctbx with external boost
493
    <dependencies>
494
      <dep package="boost"/>
942 by Marcin Wojdyr
ccp4.xml: added hdf5
495
      <dep package="hdf5"/>
1284 by Charles Ballard
try to merge in changes from series-71
496
      <dep package="h5py"/>
497
      <dep package="jinja2"/>
679 by Marcin Wojdyr
ccp4.xml & conf.py: build boost with python and cctbx with external boost
498
    </dependencies>
368 by Marcin Wojdyr
ccp4.xml: use custom module type for cctbx
499
  </custom>
63 by Marcin Wojdyr
updated ccp4-jhbuild
500
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
501
  <repository type="tarball" name="pre_ftp"
502
              href="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
503
  <cmake id="pointless">
360 by Marcin Wojdyr
ccp4.xml: switch pointless to light checkout (normal checkout can be long)
504
    <branch light="yes"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
505
    <dependencies>
506
      <dep package="clipper"/>
507
      <dep package="libccp4"/>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
508
      <dep package="cctbx-phaser"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
509
    </dependencies>
510
  </cmake>
511
512
  <cmake id="aimless">
303 by Marcin Wojdyr
moduleset: take pointless and aimless from bazaar
513
    <branch/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
514
    <dependencies>
515
      <dep package="clipper"/>
516
      <dep package="libccp4"/>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
517
      <dep package="cctbx-phaser"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
518
    </dependencies>
519
  </cmake>
520
670 by Charles Ballard
trunk gets feckless build
521
  <cmake id="feckless">
672 by Marcin Wojdyr
ccp4.xml: fix 'feckless' entry
522
    <branch/>
670 by Charles Ballard
trunk gets feckless build
523
    <dependencies>
524
      <dep package="clipper"/>
525
      <dep package="libccp4"/>
526
      <dep package="cctbx-phaser"/>
527
    </dependencies>
528
  </cmake>
529
1040 by Marcin Wojdyr
ccp4.xml: use cmake for clipper-progs
530
  <cmake id="clipper-progs">
62 by Marcin Wojdyr
updated ccp4-jhbuild
531
    <branch/>
56 by Marcin Wojdyr
a few small updates
532
    <dependencies>
533
      <dep package="clipper"/>
534
      <dep package="libccp4"/>
535
    </dependencies>
1040 by Marcin Wojdyr
ccp4.xml: use cmake for clipper-progs
536
  </cmake>
56 by Marcin Wojdyr
a few small updates
537
192 by Marcin Wojdyr
cprodrg is now in bzr, CVS no longer needed
538
  <autotools id="cprodrg">
539
    <branch/>
42 by Marcin Wojdyr
added cmake script for aimless, fixed autogen.sh for cctbx
540
    <dependencies>
69 by Marcin Wojdyr
added some system packages to the build (like zlib)
541
      <dep package="zlib"/>
42 by Marcin Wojdyr
added cmake script for aimless, fixed autogen.sh for cctbx
542
      <dep package="libccp4"/>
543
    </dependencies>
544
  </autotools>
545
794 by Marcin Wojdyr
ccp4.xml: build prosmart using cmake
546
  <cmake id="prosmart">
79 by Marcin Wojdyr
ccp4.xml: added prosmart and updated ccp4-progs
547
    <branch/>
1257.1.18 by Tom Burnley
add mmdb2 as dep. for prosmart
548
    <dependencies>
549
      <dep package="mmdb2"/>
550
    </dependencies>
794 by Marcin Wojdyr
ccp4.xml: build prosmart using cmake
551
  </cmake>
79 by Marcin Wojdyr
ccp4.xml: added prosmart and updated ccp4-progs
552
885 by Marcin Wojdyr
ccp4.xml: added restraint-valid, whatever it is, just for download
553
  <custom id="restraint-valid">
554
    <branch/>
555
  </custom>
556
792 by Marcin Wojdyr
ccp4.xml: added acedrg
557
  <cmake id="acedrg">
795 by Marcin Wojdyr
ccp4.xml: acedrg - use light checkout
558
    <branch light="yes"/>
792 by Marcin Wojdyr
ccp4.xml: added acedrg
559
    <dependencies>
1073 by Charles Ballard
ccp4i2 dependencies biopython and jsrview are reinstated.
560
       <dep package="rdkit"/>
792 by Marcin Wojdyr
ccp4.xml: added acedrg
561
    </dependencies>
562
  </cmake>
563
906 by Marcin Wojdyr
ccp4.xml: add libg
564
  <cmake id="libg">
565
    <branch/>
566
  </cmake>
567
858 by Marcin Wojdyr
ccp4.xml: add privateer
568
  <cmake id="privateer">
569
    <branch/>
570
    <dependencies>
571
      <dep package="clipper"/>
1129 by Marcin Wojdyr
ccp4.xml: privateer now depends on ccp4srs
572
      <dep package="ccp4srs"/>
858 by Marcin Wojdyr
ccp4.xml: add privateer
573
    </dependencies>
574
  </cmake>
575
47 by Marcin Wojdyr
updated modules list (not tested)
576
  <autotools id="rapper">
628 by Marcin Wojdyr
change rapper tarball, added fix for building with static libxml2
577
    <branch repo="files" module="rapper_ccp4-1.0a.tar.bz2"
578
            size="11337826" version="1.0a"/>
132 by Marcin Wojdyr
updated moduleset
579
    <dependencies>
580
      <dep package="libxml2"/>
581
      <dep package="gc"/>
582
    </dependencies>
47 by Marcin Wojdyr
updated modules list (not tested)
583
  </autotools>
584
215 by Marcin Wojdyr
misc. changes in conf.py and ccp4.xml
585
  <autotools id="diff-image">
172 by Marcin Wojdyr
updated moduleset
586
    <branch/>
115 by Marcin Wojdyr
moduleset: updated diff-image options
587
    <dependencies>
588
      <dep package="libjpeg"/>
122 by Marcin Wojdyr
added ccp4mapwish module
589
    </dependencies>
704 by Marcin Wojdyr
build ccp4mapwish and diff-image after tcltk84
590
    <after>
591
      <dep package="tcltk84"/>
592
    </after>
122 by Marcin Wojdyr
added ccp4mapwish module
593
  </autotools>
594
595
  <autotools id="ccp4mapwish">
596
    <branch/>
597
    <dependencies>
598
      <dep package="libccp4"/>
115 by Marcin Wojdyr
moduleset: updated diff-image options
599
    </dependencies>
704 by Marcin Wojdyr
build ccp4mapwish and diff-image after tcltk84
600
    <after>
601
      <!-- it requires Tcl, but on Windows Tcl must be installed manually -->
602
      <dep package="tcltk84"/>
603
    </after>
88 by Marcin Wojdyr
update c-j
604
  </autotools>
605
1172 by Marcin Wojdyr
crank: use only branch 2.0
606
  <cmake id="crank2" cmakeargs="-DCMAKE_BUILD_TYPE=None">
1288 by Charles Ballard
crank2 sites in crank
607
    <branch module="crank"/>
686 by Marcin Wojdyr
ccp4.xml: added crank2
608
    <dependencies>
1172 by Marcin Wojdyr
crank: use only branch 2.0
609
      <dep package="libccp4"/>
610
      <dep package="clipper"/>
611
      <dep package="lapack"/>
1027 by Marcin Wojdyr
ccp4.xml: exclude biopython and jsrview from default
612
      <!--<dep package="jsrview"/>-->
686 by Marcin Wojdyr
ccp4.xml: added crank2
613
    </dependencies>
614
  </cmake>
615
627 by Marcin Wojdyr
ccp4.xml: add blend
616
  <cmake id="blend">
617
    <branch/>
618
    <dependencies>
619
      <dep package="clipper"/>
620
      <dep package="cctbx-phaser"/>
621
    </dependencies>
622
  </cmake>
623
527 by Marcin Wojdyr
add chooch, but don't build it
624
  <cmake id="chooch">
625
    <branch/>
626
    <dependencies>
627
      <dep package="gsl"/>
588 by Marcin Wojdyr
ccp4.xml: added plplot
628
      <dep package="plplot"/>
527 by Marcin Wojdyr
add chooch, but don't build it
629
    </dependencies>
630
  </cmake>
631
1294 by Charles Ballard
add whatcheck cmakeargs for linux
632
  <cmake id="whatcheck" cmakeargs="-DCMAKE_Fortran_FLAGS='-DBSLASH1' -DCMAKE_C_FLAGS='-DCTEXT'" >
1284 by Charles Ballard
try to merge in changes from series-71
633
    <branch repo="files" module="whatcheck${version}.tar.bz2"
634
            checkoutdir="whatcheck"
1291 by Charles Ballard
update size of whatcheck
635
            size="106278030" version="15">
1284 by Charles Ballard
try to merge in changes from series-71
636
      <patch file="whatcheck-cmake.patch" strip="0" />
637
    </branch>
638
  </cmake>
639
647 by ronan.keegan at ac
added spicker build
640
  <cmake id="spicker">
641
    <branch/>
642
  </cmake>
643
742 by ronan.keegan at ac
Added prelyscar to build
644
  <cmake id="prelyscar">
645
    <branch/>
646
  </cmake>
647
1112 by Marcin Wojdyr
new theseus CMakeLists.txt
648
  <repository type="tarball" name="theseus3d"
649
              href="http://www.theseus3d.org/src/"/>
652 by ronan.keegan at ac
Added theseus 2.0.6 to the build
650
  <cmake id="theseus">
1318 by Charles Ballard
as cannot get to http://www.theseus3d.org use local copy
651
    <branch repo="files" module="theseus_${version}.tar.gz" version="3.3.0"
1112 by Marcin Wojdyr
new theseus CMakeLists.txt
652
            size="22548124" checkoutdir="theseus_${version}">
653
      <patch file="theseus.patch" strip="0" />
654
    </branch>
652 by ronan.keegan at ac
Added theseus 2.0.6 to the build
655
    <dependencies>
656
      <dep package="gsl"/>
657
    </dependencies>
658
  </cmake>
659
539 by Marcin Wojdyr
ccp4.xml: added clustalw2, preparing mafft
660
  <!-- Unix-only (relies on shell-scripting inside system() call) -->
661
  <!-- <repository type="tarball" name="pdb-extract"
662
              href="http://sw-tools.pdb.org/apps/PDB_EXTRACT/"/> -->
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
663
  <custom id="pdb-extract" build="make" clean="make clean"
263 by Marcin Wojdyr
use xia2 from svn (again), avoid copying .bzr/.svn dirs on install
664
                           install_to="bin/* bin/">
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
665
    <!-- <branch module="pdb-extract-v3.11-prod-src.tar.gz" repo="pdb-extract"
539 by Marcin Wojdyr
ccp4.xml: added clustalw2, preparing mafft
666
               version="3.11"/> - original tarball doesn't compile of-of-box
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
667
    -->
668
    <branch/>
669
  </custom>
101 by Marcin Wojdyr
updated ccp4-jhbuild
670
880 by Marcin Wojdyr
add HMMER
671
  <repository type="tarball" name="hmmer"
1181 by ronan.keegan at ac
updated mrbump installer and update to hmmer location
672
              href="http://eddylab.org/software/"/>
880 by Marcin Wojdyr
add HMMER
673
  <autotools id="hmmer" autogenargs="--bindir=${prefix}/libexec --enable-sse">
674
    <branch repo="hmmer" module="hmmer3/3.1b1/hmmer-3.1b1.tar.gz"
675
            version="3.1b1" size="5778584"/>
676
  </autotools>
677
539 by Marcin Wojdyr
ccp4.xml: added clustalw2, preparing mafft
678
  <repository type="tarball" name="clustal"
679
              href="http://www.clustal.org/download/current/"/>
680
  <autotools id="clustalw2" autogenargs="--bindir=${prefix}/libexec">
681
    <branch repo="clustal" module="clustalw-2.1.tar.gz"
544 by Marcin Wojdyr
added clustalw2 patch for MinGW, finishing mafft setup
682
            version="2.1" size="350761">
683
      <patch file="clustalw2-time.patch" strip="0" />
662 by Charles Ballard
need string header for clang-5
684
      <patch file="clustalw2-string.patch" strip="0" />
544 by Marcin Wojdyr
added clustalw2 patch for MinGW, finishing mafft setup
685
    </branch>
539 by Marcin Wojdyr
ccp4.xml: added clustalw2, preparing mafft
686
  </autotools>
687
688
  <repository type="tarball" name="mafft"
689
              href="http://mafft.cbrc.jp/alignment/software/"/>
1103 by Marcin Wojdyr
update mafft
690
  <!-- "make -e" overrides CC and CFLAGS in Makefile 
691
       (we could do "sed -i 's/^C/#C/' core/Makefile" instead).
692
       sed hack is needed because BINDIR is the same as  LIBDIR
544 by Marcin Wojdyr
added clustalw2 patch for MinGW, finishing mafft setup
693
  -->
694
  <custom id="mafft"
822 by Marcin Wojdyr
updated mafft
695
      configure="sed -i.bak 's/^rm.*ln -s.*[.]/true/' core/Makefile"
955 by Marcin Wojdyr
ccp4.xml: add -j1 to mafft "make clean all" - parallel results are undefined
696
      build="${} -e -C core -j1 clean all"
1103 by Marcin Wojdyr
update mafft
697
      install="make -C core install DESTDIR=${destdir} PREFIX=${prefix} LIBDIR=${prefix}/libexec BINDIR=${prefix}/libexec"
544 by Marcin Wojdyr
added clustalw2 patch for MinGW, finishing mafft setup
698
      clean="make -C core clean">
896 by Marcin Wojdyr
ccp4.xml: update mafft
699
    <branch repo="mafft" module="mafft-${version}-without-extensions-src.tgz"
700
            checkoutdir="mafft-${version}-without-extensions"
1103 by Marcin Wojdyr
update mafft
701
            version="7.245" size="397503"/>
539 by Marcin Wojdyr
ccp4.xml: added clustalw2, preparing mafft
702
  </custom>
703
320 by Marcin Wojdyr
more coot dependencies
704
<!--
705
install intltool libfontconfig1-dev libxrender-dev
706
(libxinerama-dev)
392 by Marcin Wojdyr
minor doc updates
707
(glut.m4 wants libxmu-dev)
320 by Marcin Wojdyr
more coot dependencies
708
-->
329 by Marcin Wojdyr
ccp4.xml: added guile-gtk, guile-gui, oldssm
709
  <repository type="tarball" name="mrc_coot"
428 by Marcin Wojdyr
coot: updated URL, added --includedir
710
              href="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
711
  <custom id="coot-reference-structures"
712
          install_to="* share/coot/reference-structures/">
329 by Marcin Wojdyr
ccp4.xml: added guile-gtk, guile-gui, oldssm
713
    <branch repo="mrc_coot" module="dependencies/reference-structures.tar.gz"
714
            version="0" size="6728787"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
715
  </custom>
329 by Marcin Wojdyr
ccp4.xml: added guile-gtk, guile-gui, oldssm
716
  <autotools id="guile-gui">
717
    <branch repo="mrc_coot" module="dependencies/guile-gui-0.3.tar.gz"
718
            version="0.3" size="68535"/>
719
    <dependencies>
720
      <dep package="guile-gtk"/>
721
    </dependencies>
722
  </autotools>
723
333 by Marcin Wojdyr
ccp4.xml: another pango flag and added non-working module greg
724
  <!-- not really needed, nor working -->
725
  <autotools id="greg">
726
    <branch repo="mrc_coot" module="dependencies/greg-2.0.0-pe.tar.gz"
727
            version="2.0.0" size="453770"/>
728
    <dependencies>
729
      <dep package="guile"/>
730
    </dependencies>
731
  </autotools>
732
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
733
  <autotools id="coot" autogen-sh="configure"
1307 by Charles Ballard
correct co location, and update RDKit library names in coot build
734
             autogenargs="--with-enhanced-ligand-tools --with-guile --with-python --with-pygtk --with-goocanvas-prefix=${prefix} --with-guile-gtk --includedir=${prefix}/include/coot RDKIT_CXXFLAGS=-I${prefix}/include/rdkit RDKIT_LIBS='-lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitMolChemicalFeatures -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDepictor -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDistGeomHelpers -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7' COOT_BUILD_INFO_STRING='CCP4, Oxfordshire'">
832 by Marcin Wojdyr
add coot prerelease, for now as coot-0.8
735
    <branch repo="mrc_coot"
1249 by Charles Ballard
update coot version to 0.8.8
736
            module="source/releases/coot-${version}.tar.gz"
737
            checkoutdir="coot-${version}" size="19472776" version="0.8.8">
887 by Marcin Wojdyr
updated coot
738
      <patch file="coot-coot-in.patch" strip="0" />
832 by Marcin Wojdyr
add coot prerelease, for now as coot-0.8
739
      <patch file="coot-syminfo.patch" strip="0" />
834 by Marcin Wojdyr
updated coot-0.8
740
      <patch file="coot-main-title.patch" strip="0"/>
1109 by Marcin Wojdyr
patch coot to make it work with RDKit 2015.03
741
      <patch file="coot-unfog-bitmap.patch" strip="0"/>
1216 by Charles Ballard
update for coot 0.8.6
742
      <patch file="coot-view.patch" strip="0"/>
1284 by Charles Ballard
try to merge in changes from series-71
743
      <patch file="coot-rdkit-interface.patch" strip="0"/>
744
      <patch file="coot-callbacks.patch" strip="0"/>
832 by Marcin Wojdyr
add coot prerelease, for now as coot-0.8
745
    </branch>
746
    <dependencies>
747
      <dep package="ssm"/>
887 by Marcin Wojdyr
updated coot
748
      <!-- dep package="ccp4srs"/> coot w/ SRS crashes.
749
                       When ready, add -with-ccp4srs-prefix=${prefix}  -->
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
750
      <dep package="mmdb2"/>
832 by Marcin Wojdyr
add coot prerelease, for now as coot-0.8
751
      <dep package="clipper"/>
752
      <dep package="monomers"/>
753
      <dep package="coot-reference-structures"/>
754
      <dep package="curl"/>
755
      <dep package="gsl"/>
756
      <dep package="goocanvas"/>
757
      <dep package="libgnomecanvas"/>
758
      <dep package="pygtk"/>
759
      <dep package="librsvg"/>
760
      <dep package="gtkglext"/>
761
      <dep package="guile"/>
762
      <dep package="guile-gui"/>
763
      <dep package="guile-lib"/>
764
      <dep package="freeglut"/>
765
      <dep package="libglade"/>
766
      <dep package="rdkit"/>
887 by Marcin Wojdyr
updated coot
767
      <dep package="sqlite3"/>
832 by Marcin Wojdyr
add coot prerelease, for now as coot-0.8
768
    </dependencies>
769
  </autotools>
770
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
771
  <!-- non-crystallographic dependencies -->
772
988 by Marcin Wojdyr
tcltk84: build it out-of-source, make it use $LDFLAGS on Linux
773
  <custom id="tcltk84" configure="true" install="${srcdir}/build.sh ${dest}"
774
          clean="rm -rf build/" supports-non-srcdir-builds="yes">
324 by Marcin Wojdyr
updated coot version
775
    <branch repo="files" module="tcltk++_${version}.tar.gz"
1322 by Charles Ballard
mysterious size change on 9 Oct 2017
776
            version="8.4.20.3" size="17968604">
514 by Charles Ballard
wrong strip level on patch
777
      <patch file="tcltk84-configure.patch" strip="0" />
324 by Marcin Wojdyr
updated coot version
778
    </branch>
779
  </custom>
780
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
781
  <repository type="tarball" name="cmake" href="http://www.cmake.org/files/"/>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
782
  <autotools id="cmake"
783
             autogen-template="%(srcdir)s/bootstrap --prefix=%(prefix)s">
1044 by Marcin Wojdyr
update cmake to 3.1.3
784
    <branch module="v3.1/cmake-${version}.tar.gz"
785
            repo="cmake" version="3.1.3" size="5959549">
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
786
    </branch>
787
  </autotools>
788
352 by Marcin Wojdyr
ccp4.xml: added pkgconf
789
  <repository type="tarball" name="pkgconf"
790
               href="http://rabbit.dereferenced.org/~nenolod/distfiles/"/>
665 by Marcin Wojdyr
ccp4.xml: updated pkgconf
791
  <autotools id="pkgconf" autogenargs="--bindir=${prefix}/devbin">
792
    <branch repo="pkgconf" module="pkgconf-${version}.tar.gz"
828 by Marcin Wojdyr
updated pkgconf
793
            version="0.9.6" size="98886"/>
352 by Marcin Wojdyr
ccp4.xml: added pkgconf
794
  </autotools>
795
1041 by Marcin Wojdyr
bootstrap patchelf on Linux
796
  <repository type="tarball" name="nixos" href="http://nixos.org/releases/"/>
797
  <autotools id="patchelf" autogenargs="--bindir=${prefix}/devbin">
798
    <branch repo="nixos" module="patchelf/patchelf-0.8/patchelf-0.8.tar.gz"
799
            version="0.8" size="144271"/>
800
  </autotools>
801
489 by Marcin Wojdyr
moduleset: added libgnurx (for testing)
802
  <autotools id="libgnurx">
803
    <branch repo="files" module="libgnurx-2.5.1.tar.gz"
492 by Marcin Wojdyr
ccp4.xml: changes in libgnurx
804
            version="2.5.1" size="379950"/>
489 by Marcin Wojdyr
moduleset: added libgnurx (for testing)
805
  </autotools>
806
306 by Marcin Wojdyr
added more coot dependencies
807
  <repository type="tarball" name="tukaani" href="http://tukaani.org/"/>
808
  <autotools id="xz" autogen-sh="configure" autogenargs="--disable-rpath">
809
    <branch repo="tukaani" module="xz/xz-5.0.4.tar.gz"
810
            version="5.0.4" size="1281166">
811
    </branch>
812
  </autotools>
813
821 by Marcin Wojdyr
ccp4.xml: update rdkit
814
  <!-- we don't need python bindings, but -DRDK_BUILD_PYTHON_WRAPPERS=OFF
815
     prevents installing some headers that are included from other headers -->
1132 by Marcin Wojdyr
ccp4.xml: add -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=${prefix} for rdkit
816
  <cmake id="rdkit" cmakeargs="-DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_SLN_SUPPORT=OFF -DRDK_TEST_MMFF_COMPLIANCE=OFF -DRDK_BUILD_CPP_TESTS=OFF -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=${prefix}">
1284 by Charles Ballard
try to merge in changes from series-71
817
  <if condition-set="mingw">
818
    <cmakeargs value="-DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_SLN_SUPPORT=OFF -DRDK_TEST_MMFF_COMPLIANCE=OFF -DRDK_BUILD_CPP_TESTS=OFF -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_ROOT=${prefix} -DRDK_USE_BOOST_SERIALIZATION=OFF -DRDK_BUILD_THREADSAFE_SSS=OFF " />
819
  </if>
1245 by Charles Ballard
update RDKit to 2016_09_04
820
    <branch module="rdkit/rdkit/archive/Release_${version}.tar.gz"
1284 by Charles Ballard
try to merge in changes from series-71
821
            repo="github-zip" version="2017_03_2" size="27110625"
1097 by Marcin Wojdyr
update RDKit
822
            checkoutdir="rdkit-Release_${version}">
1147 by Charles Ballard
patch for rdkit 2015_03_01 as mingw already has timezone defined
823
      <patch file="rdkit-DebugTrace-mingw.patch" strip="0" />
334 by Marcin Wojdyr
ccp4.xml: added rdkit
824
    </branch>
821 by Marcin Wojdyr
ccp4.xml: update rdkit
825
    <dependencies>
826
      <dep package="boost"/>
827
      <dep package="numpy"/>
828
      <dep package="sqlite3"/>
829
    </dependencies>
334 by Marcin Wojdyr
ccp4.xml: added rdkit
830
  </cmake>
831
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
832
  <repository type="tarball" name="bitbucket" href="https://bitbucket.org/"/>
833
  <autotools id="libgd" autogen-sh="configure"
1146 by Marcin Wojdyr
libgd: update 2.1.0 -> 2.1.1 and add option --without-vpx
834
             autogenargs="--with-png --with-jpeg --with-freetype --without-tiff --without-xpm --without-vpx --bindir=${prefix}/devbin">
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
835
    <branch repo="bitbucket"
331 by Marcin Wojdyr
updated libgd and python, added patch for coot
836
            module="libgd/gd-libgd/downloads/libgd-${version}.tar.bz2"
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
837
            checkoutdir="libgd-${version}"
1146 by Marcin Wojdyr
libgd: update 2.1.0 -> 2.1.1 and add option --without-vpx
838
            version="2.1.1" size="2308977">
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
839
    </branch>
840
    <dependencies>
841
      <dep package="libpng"/>
842
      <dep package="libjpeg"/>
843
    </dependencies>
403 by Marcin Wojdyr
ccp4.xml: add pkgconf to ccp4-windows
844
    <after>
845
      <dep package="pkgconf"/>
547 by Marcin Wojdyr
ccp4.xml: cosmetic changes
846
      <dep package="freetype2"/>
403 by Marcin Wojdyr
ccp4.xml: add pkgconf to ccp4-windows
847
    </after>
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
848
  </autotools>
306 by Marcin Wojdyr
added more coot dependencies
849
752 by Marcin Wojdyr
add sqlite3 (for Linux)
850
  <repository type="tarball" name="sqlite" href="http://sqlite.org/"/>
851
  <autotools id="sqlite3"
852
     autogenargs="--bindir=${prefix}/devbin CFLAGS=&quot;$CFLAGS -DSQLITE_ENABLE_FTS3=1 -DSQLITE_ENABLE_COLUMN_METADATA=1 -DSQLITE_ENABLE_UNLOCK_NOTIFY=1 -DSQLITE_SECURE_DELETE=1&quot;">
1104 by Marcin Wojdyr
update sqlite to 3.8.11.1
853
    <branch repo="sqlite" module="2015/sqlite-autoconf-3081101.tar.gz"
854
            version="3.8.11.1" size="2101885"/>
752 by Marcin Wojdyr
add sqlite3 (for Linux)
855
  </autotools>
856
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
857
  <repository type="tarball" name="python"
858
              href="http://www.python.org/ftp/python/"/>
455 by Marcin Wojdyr
introduced directory devbin/ for binaries not needed after bulding is done
859
  <autotools id="python" autogenargs="--bindir=${prefix}/libexec">
1342 by ccp4
add conditional for ucs4 and plplot CMAKE_INSTALL_LIBDIR
860
  <if condition-set="ucs4">
861
    <autogenargs value="--bindir=${prefix}/libexec --enable-unicode=ucs4 "/>
862
  </if>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
863
    <pkg-config>python-2.7.pc</pkg-config>
1191 by Marcin Wojdyr
update python to 2.7.11
864
    <branch module="2.7.11/Python-2.7.11.tgz"
865
            repo="python" version="2.7.11" size="16856409">
591 by Charles Ballard
patch python build on os x
866
      <patch file="python-2.7.6-osx.patch" strip="0" />
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
867
    </branch>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
868
    <dependencies>
869
      <dep package="zlib"/>
870
      <dep package="bzip2"/>
871
      <dep package="openssl"/>
752 by Marcin Wojdyr
add sqlite3 (for Linux)
872
      <dep package="sqlite3"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
873
    </dependencies>
1257.1.21 by Colin Palmer
Add readline as a soft dependency for python
874
    <suggests>
875
      <dep package="readline"/>
876
    </suggests>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
877
  </autotools>
878
112 by Marcin Wojdyr
updated moduleset (zlib and refmac-dictionary)
879
  <cmake id="zlib">
308 by Marcin Wojdyr
ccp4.xml: update zlib
880
    <!-- both dynamic and static libraries are built -->
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
881
    <pkg-config>zlib.pc</pkg-config>
308 by Marcin Wojdyr
ccp4.xml: update zlib
882
    <branch repo="sf" module="libpng/zlib-1.2.8.tar.gz"
883
            version="1.2.8" size="571091"/>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
884
  </cmake>
885
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
886
  <repository type="tarball" name="sbrabec"
887
              href="http://ftp.suse.com/pub/people/sbrabec/"/>
455 by Marcin Wojdyr
introduced directory devbin/ for binaries not needed after bulding is done
888
  <autotools id="bzip2" autogenargs="--bindir=${prefix}/devbin">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
889
    <pkg-config>bzip2.pc</pkg-config>
890
    <!-- using autotool-ized tarball from Suse -->
891
    <branch repo="sbrabec" module="bzip2/tarballs/bzip2-1.0.6.0.1.tar.gz"
892
            version="1.0.6" size="1071724">
893
    </branch>
894
  </autotools>
895
896
  <repository type="tarball" name="openssl"
1226 by Marcin Wojdyr
update openssl as requested by Martyn, the old version is no longer on ftp
897
              href="https://www.openssl.org/source/"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
898
  <custom id="openssl"
888 by Marcin Wojdyr
ccp4.xml: updating openssl, hoping it will fix build problem on windows
899
          configure="./config --prefix=${prefix} --openssldir=${prefix}/etc/openssl no-hw shared"
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
900
          build="make" clean="make clean"
637 by Marcin Wojdyr
ccp4.xml, openssl: skip building docs (it fails with new pod2html)
901
          install="touch install_docs; make INSTALL_PREFIX=${destdir} install">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
902
    <pkg-config>openssl.pc</pkg-config>
903
    <branch repo="openssl" module="openssl-${version}.tar.gz"
1226 by Marcin Wojdyr
update openssl as requested by Martyn, the old version is no longer on ftp
904
            version="1.0.2j" size="5307912">
987 by Marcin Wojdyr
update openssl + patch for linking libgost.so
905
     <patch file="openssl-ldflags.patch" strip="0" />
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
906
    </branch>
907
    <dependencies>
908
      <dep package="zlib"/>
909
    </dependencies>
910
  </custom>
911
912
  <repository type="tarball" name="curl" href="http://curl.haxx.se/download/"/>
455 by Marcin Wojdyr
introduced directory devbin/ for binaries not needed after bulding is done
913
  <autotools id="curl" autogenargs="--disable-manual --disable-ldap --bindir=${prefix}/devbin">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
914
    <pkg-config>libcurl.pc</pkg-config>
915
    <branch module="curl-${version}.tar.gz"
876 by Marcin Wojdyr
update curl to 7.37.1 -- 7.30 doesn't build with the latest icc (15) on Linux
916
            repo="curl" version="7.37.1" size="4076296">
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
917
     <patch file="curl-configure.patch" strip="0" />
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
918
    </branch>
319 by Marcin Wojdyr
ccp4.xml: more coot dependencies
919
    <dependencies>
920
      <dep package="openssl"/>
921
    </dependencies>
922
  </autotools>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
923
924
  <repository type="tarball" name="gnu" href="ftp://ftp.gnu.org/"/>
920 by Marcin Wojdyr
update gsl
925
  <!-- MINGW=true is a hack to link gsl with gslcblas and avoid problems
926
       when programs are linked with -as-needed -->
1267 by Charles Ballard
use autogen.sh -> configure for gsl
927
  <autotools id="gsl" autogenargs="MINGW=true"
928
    autogen-sh="configure" >
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
929
    <pkg-config>gsl.pc</pkg-config>
930
    <branch repo="gnu" module="gnu/gsl/gsl-${version}.tar.gz"
920 by Marcin Wojdyr
update gsl
931
            version="1.16" size="3534080"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
932
  </autotools>
933
329 by Marcin Wojdyr
ccp4.xml: added guile-gtk, guile-gui, oldssm
934
  <autotools id="guile-gtk" autogenargs="--without-glade --without-gtkgl">
935
    <branch repo="gnu" module="gnu/guile-gtk/guile-gtk-2.1.tar.gz"
936
            version="2.1" size="781985"/>
937
    <dependencies>
938
      <dep package="guile"/>
939
      <dep package="gtk2"/>
940
    </dependencies>
941
  </autotools>
942
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
943
  <repository type="tarball" name="gnome"
477 by Marcin Wojdyr
changed gnome download URL (the previous one didn't work with curl on OSX)
944
              href="http://ftp.gnome.org/pub/gnome/sources/"/>
306 by Marcin Wojdyr
added more coot dependencies
945
  <autotools id="libgnomecanvas" autogen-sh="configure" autogenargs="">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
946
    <pkg-config>libgnomecanvas-2.0.pc</pkg-config>
947
    <branch repo="gnome"
948
            module="libgnomecanvas/2.30/libgnomecanvas-${version}.tar.bz2"
949
            version="2.30.3" size="574139"/>
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
950
    <!--branch repo="gnome"
951
            module="libgnomecanvas/2.20/libgnomecanvas-${version}.tar.bz2"
952
            version="2.20.1" size="583613"/-->
319 by Marcin Wojdyr
ccp4.xml: more coot dependencies
953
    <dependencies>
954
      <dep package="gtk2"/>
955
      <dep package="libart_lgpl"/>
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
956
      <!--dep package="libglade"/-->
319 by Marcin Wojdyr
ccp4.xml: more coot dependencies
957
    </dependencies>
958
  </autotools>
959
  <autotools id="libart_lgpl" autogen-sh="configure" autogenargs="">
960
    <branch repo="gnome"
961
            module="libart_lgpl/2.3/libart_lgpl-${version}.tar.bz2"
962
            version="2.3.21" size="329102"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
963
  </autotools>
884 by Marcin Wojdyr
ccp4.xml: goocanvas: "make" only in src, to avoid problem with linking demos
964
  <autotools id="goocanvas" autogen-sh="configure" autogenargs=""
965
             makeargs="SUBDIRS=src"
966
             makeinstallargs="SUBDIRS=src install">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
967
    <pkg-config>goocanvas.pc</pkg-config>
968
    <branch repo="gnome" module="goocanvas/1.0/goocanvas-1.0.0.tar.bz2"
969
            version="1.0.0" size="570552"/>
317 by Marcin Wojdyr
minor updates
970
    <dependencies>
971
      <dep package="gtk2"/>
972
      <dep package="cairo"/>
973
    </dependencies>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
974
  </autotools>
975
  <autotools id="pygtk" autogenargs="--without-glade">
976
    <branch repo="gnome" module="pygtk/2.24/pygtk-2.24.0.tar.bz2"
977
            version="2.24.0" size="2361097"/>
978
    <dependencies>
979
      <dep package="pygobject2"/>
980
      <dep package="py2cairo"/>
981
    </dependencies>
982
  </autotools>
983
  <autotools id="pygobject2" autogenargs="--disable-introspection">
984
    <branch repo="gnome" module="pygobject/2.28/pygobject-2.28.6.tar.bz2"
985
            version="2.28.6" size="888240"/>
322 by Marcin Wojdyr
adding dependencies, patch for libffi
986
    <dependencies>
987
      <dep package="glib"/>
988
      <dep package="py2cairo"/>
989
    </dependencies>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
990
  </autotools>
306 by Marcin Wojdyr
added more coot dependencies
991
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
992
  <repository type="tarball" name="cairo" href="http://cairographics.org/"/>
986 by Marcin Wojdyr
ccp4.xml: build cairo with --disable-trace (to make it simpler)
993
  <autotools id="cairo" autogen-sh="configure"
994
              autogenargs="--enable-xlib --disable-trace">
306 by Marcin Wojdyr
added more coot dependencies
995
    <pkg-config>cairo.pc</pkg-config>
996
    <!--
997
    <branch repo="cairo" module="releases/cairo-1.8.10.tar.gz"
998
            version="1.8.10" size="7102657"/>
999
    -->
1000
    <branch repo="cairo" module="releases/cairo-1.10.2.tar.gz"
1001
            version="1.10.2" size="23558405"/>
1002
    <dependencies>
1003
      <dep package="pixman"/>
320 by Marcin Wojdyr
more coot dependencies
1004
      <dep package="libpng"/>
306 by Marcin Wojdyr
added more coot dependencies
1005
    </dependencies>
894 by Marcin Wojdyr
ccp4.xml: cairo after freetype2
1006
    <after>
1007
      <dep package="freetype2"/>
1008
    </after>
306 by Marcin Wojdyr
added more coot dependencies
1009
  </autotools>
1336 by Charles Ballard
arcimboldo on osx and linux only
1010
1011
  <!-- Try disable-mmx due to compile errors on Mac see:
1012
    https://github.com/Homebrew/legacy-homebrew/issues/41056 -->
306 by Marcin Wojdyr
added more coot dependencies
1013
  <autotools id="pixman" autogen-sh="configure" autogenargs="--disable-gtk">
1014
    <branch repo="cairo" module="releases/pixman-0.28.2.tar.gz"
1015
            version="0.28.2" size="734094"/>
1016
    <dependencies>
1017
    </dependencies>
1018
  </autotools>
1019
839 by Marcin Wojdyr
ccp4.xml: added intltool
1020
  <autotools id="intltool" autogenargs="--bindir=${prefix}/devbin">
1021
    <branch repo="lp" module="intltool/trunk/0.50.2/+download/intltool-${version}.tar.gz"
1022
            version="0.50.2" size="189483"/>
1023
  </autotools>
1024
833 by Marcin Wojdyr
ccp4.xml: gettext: avoid checking for Java (and popup message on OSX)
1025
  <!-- only libintl.dylib is used by glib
1026
       GCJ=none is set to avoid checking java and OSX popup  -->
815 by Marcin Wojdyr
ccp4.xml: add gettext as glib dependency (for the sake of Mac)
1027
  <autotools id="gettext"
1271 by Charles Ballard
turn off git update for gettext, autogen.sh -> configure
1028
    autogenargs="--bindir=${prefix}/devbin --disable-java --disable-libasprintf --disable-curses GCJ=none"
1029
    autogen-sh="configure">
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
1030
    <branch repo="gnu" module="pub/gnu/gettext/gettext-${version}.tar.gz"
1031
            version="0.18.3.2" size="16189249"/>
1032
  </autotools>
1033
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1034
  <autotools id="py2cairo">
1035
    <branch repo="cairo" module="releases/pycairo-1.2.2.tar.gz"
306 by Marcin Wojdyr
added more coot dependencies
1036
            version="1.2.2" size="482417">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1037
    </branch>
306 by Marcin Wojdyr
added more coot dependencies
1038
    <dependencies>
1039
      <dep package="cairo"/>
1040
    </dependencies>
322 by Marcin Wojdyr
adding dependencies, patch for libffi
1041
    <after>
1042
      <dep package="python"/>
1043
    </after>
306 by Marcin Wojdyr
added more coot dependencies
1044
  </autotools>
1045
1284 by Charles Ballard
try to merge in changes from series-71
1046
  <autotools id="glib" 
1047
             autogenargs="--disable-modular-tests --disable-selinux --disable-dtrace ac_cv_func_splice=no"
1048
             autogen-sh="configure">
306 by Marcin Wojdyr
added more coot dependencies
1049
    <pkg-config>glib-2.0.pc</pkg-config>
1050
    <branch repo="gnome" module="glib/2.34/glib-2.34.3.tar.xz"
850 by Marcin Wojdyr
add patches/glib-osx-gcc-fix.patch: for building glib on OSX with GCC
1051
            version="2.34.3" size="6334872">
1052
      <patch file="glib-osx-gcc-fix.patch" strip="1" />
1053
    </branch>
306 by Marcin Wojdyr
added more coot dependencies
1054
    <dependencies>
320 by Marcin Wojdyr
more coot dependencies
1055
      <dep package="libffi"/>
866 by Marcin Wojdyr
ccpem dependency changed from mmdb to mmdb2
1056
      <dep package="gettext"/> <!-- skipped by default on non-OSX -->
320 by Marcin Wojdyr
more coot dependencies
1057
    </dependencies>
1058
  </autotools>
1059
835 by Marcin Wojdyr
updated cctbx-phaser to the version from 2014-05-07
1060
  <!-- ver. 3.1 has a new problem in libffi.pc.
1061
       configure patch will stay anyway to avoid ../lib64 -->
320 by Marcin Wojdyr
more coot dependencies
1062
  <repository type="tarball" name="sourceware"
1063
              href="ftp://sourceware.org/pub/"/>
1064
  <autotools id="libffi" autogenargs="--enable-portable-binary">
1065
    <pkg-config>libffi.pc</pkg-config>
1066
    <branch repo="sourceware" module="libffi/libffi-${version}.tar.gz"
322 by Marcin Wojdyr
adding dependencies, patch for libffi
1067
            version="3.0.13" size="845747">
1068
      <patch file="libffi-configure.patch" strip="1" />
769 by Charles Ballard
intel compier int128 problem pre icc 13 in libffi
1069
      <patch file="libffi_intel_define.patch" strip="0" />
322 by Marcin Wojdyr
adding dependencies, patch for libffi
1070
    </branch>
306 by Marcin Wojdyr
added more coot dependencies
1071
  </autotools>
1072
1073
  <!-- pango 1.23 requires fontconfig >= 2.5 (not on CentOS 5) -->
361 by Marcin Wojdyr
added triggers/, adjusted ccp4.xml
1074
  <!-- with included-modules there is no need to call pango-querymodules -->
306 by Marcin Wojdyr
added more coot dependencies
1075
  <autotools id="pango" autogen-sh="configure"
333 by Marcin Wojdyr
ccp4.xml: another pango flag and added non-working module greg
1076
             autogenargs="--disable-introspection --with-included-modules">
306 by Marcin Wojdyr
added more coot dependencies
1077
    <pkg-config>pango.pc</pkg-config>
1078
    <branch repo="gnome" module="pango/1.22/pango-1.22.4.tar.bz2"
1079
            version="1.22.4" size="1496168"/>
1080
    <dependencies>
1081
      <dep package="cairo"/>
486 by Marcin Wojdyr
ccp4.xml: pango requires glib
1082
      <dep package="glib"/>
306 by Marcin Wojdyr
added more coot dependencies
1083
      <!-- <dep package="harfbuzz"/> -->
1084
    </dependencies>
1085
  </autotools>
319 by Marcin Wojdyr
ccp4.xml: more coot dependencies
1086
  <autotools id="pangox" autogen-sh="configure">
1087
    <pkg-config>pangox.pc</pkg-config>
1088
    <branch repo="gnome" module="pangox-compat/0.0/pangox-compat-0.0.2.tar.xz"
1089
            version="0.0.2" size="267396"/>
1090
    <dependencies>
1091
      <dep package="pango"/>
1092
    </dependencies>
1093
  </autotools>
306 by Marcin Wojdyr
added more coot dependencies
1094
1095
  <repository type="tarball" name="freedesktop"
1096
               href="http://www.freedesktop.org/software/"/>
1097
  <autotools id="harfbuzz" autogen-sh="configure">
1098
    <pkg-config>harfbuzz.pc</pkg-config>
1099
    <branch repo="freedesktop"
1100
            module="harfbuzz/release/harfbuzz-0.9.16.tar.bz2"
1101
            version="0.9.16" size="902208"/>
1102
    <dependencies>
1103
      <dep package="glib"/>
1104
      <dep package="libicu"/>
1105
    </dependencies>
1106
  </autotools>
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
1107
  <autotools id="fontconfig" autogen-sh="configure" autogenargs="">
1108
    <pkg-config>fontconfig.pc</pkg-config>
1109
    <branch repo="freedesktop" module="fontconfig/release/fontconfig-${version}.tar.gz"
1110
            version="2.10.1" size="1700168"/>
1111
    <dependencies>
1112
      <!--<dep package="iconv"/>-->
1113
      <!--<dep package="expat"/>-->
1114
    </dependencies>
1115
  </autotools>
306 by Marcin Wojdyr
added more coot dependencies
1116
1117
  <repository type="tarball" name="icu"
1118
              href="http://download.icu-project.org/files/"/>
1119
  <autotools id="libicu" autogen-sh="source/configure"
1120
             autogenargs="--disable-tests --disable-samples --disable-rpath">
1121
    <pkg-config>icu-i18n.pc</pkg-config>
1122
    <branch repo="icu" module="icu4c/51.1/icu4c-51_1-src.tgz"
1123
            checkoutdir="libicu-51.1" version="51.1" size="21815174"/>
1124
  </autotools>
1125
1126
  <autotools id="gdk-pixbuf" autogen-sh="configure"
807 by Marcin Wojdyr
ccp4.xml: build gdk-pixbuf without gdk-pixbuf-x11 lib, which seems not used
1127
             autogenargs="--disable-introspection --without-libtiff --disable-rpath --disable-glibtest --disable-nls --with-included-loaders=png --disable-gio-sniffing">
306 by Marcin Wojdyr
added more coot dependencies
1128
    <branch repo="gnome" module="gdk-pixbuf/2.28/gdk-pixbuf-2.28.1.tar.xz"
335 by Marcin Wojdyr
added gdk-pixbuf-hack.patch
1129
            version="2.28.1" size="1191084">
1130
      <patch file="gdk-pixbuf-hack.patch" strip="0" />
1131
    </branch>
306 by Marcin Wojdyr
added more coot dependencies
1132
    <dependencies>
1133
      <dep package="libpng"/>
1134
      <dep package="libjpeg"/>
1135
      <dep package="glib"/>
1136
    </dependencies>
1137
  </autotools>
1138
1139
  <autotools id="librsvg" autogen-sh="configure"
1140
             autogenargs="--disable-introspection --disable-gtk-theme --disable-tools --disable-vala">
1141
    <!--
1142
    <branch repo="gnome" module="librsvg/2.36/librsvg-${version}.tar.xz"
1143
            version="2.36.4" size="513028"/>
1144
    -->
1145
    <branch repo="gnome" module="librsvg/2.32/librsvg-2.32.1.tar.bz2"
1146
            version="2.32.1" size="517170"/>
1147
    <dependencies>
1148
      <dep package="gdk-pixbuf"/>
1149
      <dep package="libcroco"/>
1150
    </dependencies>
1151
  </autotools>
325 by Marcin Wojdyr
workaround for libcroco -Wl,-Bsymbolic-functions error
1152
  <autotools id="libcroco" autogen-sh="configure"
1153
             autogenargs="--enable-Bsymbolic=auto">
1155 by Marcin Wojdyr
update libcroco 0.6.8 to 0.6.11
1154
    <branch repo="gnome" module="libcroco/0.6/libcroco-0.6.11.tar.xz"
1155
            version="0.6.11" size="477312"/>
306 by Marcin Wojdyr
added more coot dependencies
1156
    <dependencies>
1157
      <dep package="glib"/>
1158
      <dep package="libxml2"/>
1159
      <dep package="pango"/>
1160
    </dependencies>
1161
  </autotools>
1162
1163
  <autotools id="atk" autogen-sh="configure"
1164
             autogenargs="--disable-introspection --disable-glibtest">
1165
    <branch repo="gnome" module="atk/2.8/atk-2.8.0.tar.xz"
1166
            version="2.8.0" size="634052"/>
1167
    <dependencies>
1168
      <dep package="glib"/>
1169
    </dependencies>
1170
  </autotools>
1171
1172
  <autotools id="gtk2" autogen-sh="configure"
770 by Charles Ballard
gtk2: for none gcc compilers the visibility is a problem
1173
             autogenargs="--disable-visibility --disable-introspection --disable-glibtest --disable-cups --disable-papi --with-included-immodules">
1099 by Marcin Wojdyr
update gtk 2.24.23 to 2.24.28
1174
    <branch repo="gnome" module="gtk+/2.24/gtk+-${version}.tar.xz"
1175
            version="2.24.28" size="13354884"/>
306 by Marcin Wojdyr
added more coot dependencies
1176
    <dependencies>
1177
      <dep package="glib"/>
1178
      <dep package="cairo"/>
1179
      <dep package="pango"/>
1180
      <dep package="atk"/>
1181
      <dep package="gdk-pixbuf"/>
1182
    </dependencies>
1183
  </autotools>
361 by Marcin Wojdyr
added triggers/, adjusted ccp4.xml
1184
306 by Marcin Wojdyr
added more coot dependencies
1185
  <autotools id="gtkglext" autogen-sh="configure"
1186
             autogenargs="--disable-introspection --disable-glibtest">
319 by Marcin Wojdyr
ccp4.xml: more coot dependencies
1187
    <branch repo="gnome" module="gtkglext/1.2/gtkglext-1.2.0.tar.bz2"
1188
            version="1.2.0" size="703821">
1189
      <patch file="gtkglext-1.2.0-bz677457.diff" strip="1" />
1190
    </branch>
306 by Marcin Wojdyr
added more coot dependencies
1191
    <dependencies>
1192
      <dep package="gtk2"/>
1284 by Charles Ballard
try to merge in changes from series-71
1193
      <dep package="pangox"/>
306 by Marcin Wojdyr
added more coot dependencies
1194
    </dependencies>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1195
  </autotools>
1196
342 by Marcin Wojdyr
ccp4.xml: added libglade
1197
  <autotools id="libglade"
1198
     autogenargs="--disable-gtktest CPPFLAGS=&quot;$CPPFLAGS -UG_DISABLE_DEPRECATED&quot; --with-xml-catalog=/dev/null">
1199
    <pkg-config>libglade-2.0.pc</pkg-config>
1200
    <branch repo="gnome" module="libglade/2.6/libglade-2.6.4.tar.bz2"
1201
            version="2.6.4" size="356119"/>
1202
    <dependencies>
1203
      <dep package="gtk2"/>
1204
      <dep package="gdk-pixbuf"/>
1205
      <dep package="libxml2"/>
1206
    </dependencies>
1207
  </autotools>
1208
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1209
  <autotools id="guile" autogenargs="--disable-rpath --disable-error-on-warning">
1210
    <branch repo="gnu" module="gnu/guile/guile-1.8.8.tar.gz"
575 by Charles Ballard
the guile 1.8.8 test for stack growth direction produces effectively random results, replace with the guile-2 series test
1211
            version="1.8.8" size="3956654">
576 by Ville Uski
Add '/' on line 943 in ccp4.xml to correct a syntax error
1212
      <patch file="guile-configure.patch" strip="0"/>
808 by Marcin Wojdyr
added guile-fink.patch
1213
      <patch file="guile-fink.patch" strip="1"/>
575 by Charles Ballard
the guile 1.8.8 test for stack growth direction produces effectively random results, replace with the guile-2 series test
1214
    </branch>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1215
    <dependencies>
1216
      <dep package="libtool"/>
320 by Marcin Wojdyr
more coot dependencies
1217
      <dep package="gmp"/>
811 by Marcin Wojdyr
ccp4.xml: add readline as guile dependency
1218
      <dep package="readline"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1219
    </dependencies>
1305 by Charles Ballard
simple format fix
1220
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1221
  </autotools>
341 by Marcin Wojdyr
ccp4.xml: configure gmp with --disable-assembly (should be more portable
1222
  <autotools id="gmp" autogenargs="--disable-assembly">
320 by Marcin Wojdyr
more coot dependencies
1223
    <branch repo="gnu" module="gnu/gmp/gmp-5.1.1.tar.bz2"
1224
            version="5.1.1" size="2213841"/>
1225
  </autotools>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1226
  <autotools id="libtool" autogenargs="">
1227
    <branch repo="gnu" module="gnu/libtool/libtool-2.4.tar.gz"
1228
            version="2.4" size="2580417"/>
1229
  </autotools>
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
1230
  <autotools id="readline" autogenargs="">
1231
    <branch repo="gnu" module="gnu/readline/readline-${version}.tar.gz"
1257.1.4 by Tom Burnley
remove qtrview from ccpem deps
1232
            version="7.0" size="2910016">
812 by Marcin Wojdyr
added a patch to readline to remove -arch_only on OSX
1233
      <patch file="readline-shobj-conf.patch" strip="0"/>
1234
    </branch>
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
1235
  </autotools>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1236
1237
  <repository type="tarball" name="savannah"
1238
              href="http://download.savannah.gnu.org/releases/"/>
1239
  <autotools id="guile-lib">
1284 by Charles Ballard
try to merge in changes from series-71
1240
    <branch repo="savannah" module="guile-lib/old/guile-lib-${version}.tar.gz"
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1241
            version="0.2.2" size="476723"/>
1242
    <dependencies>
1243
      <dep package="guile"/>
1244
    </dependencies>
1245
  </autotools>
1246
1266 by Charles Ballard
switch some autogen.sh runs to configure
1247
  <autotools id="freetype2"
1248
    autogen-sh="configure" >
353 by Marcin Wojdyr
ccp4.xml: added freetype2
1249
    <pkg-config>freetype2.pc</pkg-config>
1209 by Marcin Wojdyr
take freetype from SF instead of Savannah, because:
1250
    <branch repo="sf" module="freetype/freetype-${version}.tar.bz2"
1192 by Marcin Wojdyr
minor freetype update 2.5.3 -> 2.5.5
1251
            version="2.5.5" size="1714529"/>
353 by Marcin Wojdyr
ccp4.xml: added freetype2
1252
  </autotools>
1253
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1254
  <repository type="tarball" name="pypi"
1300 by ccp4
update location of pypi branches
1255
              href="https://pypi.python.org/packages/"/>
931 by Marcin Wojdyr
ccp4.xml: add --install-scripts=${prefix}/libexec for easyinstall, pip, bzr
1256
  <distutils id="setuptools" installargs="--install-scripts=${prefix}/libexec">
1300 by ccp4
update location of pypi branches
1257
    <branch repo="pypi" module="source/s/setuptools/setuptools-${version}.tar.gz"
613 by Marcin Wojdyr
ccp4.xml: added more ccp4mg dependencies: suds, lxml, libxslt,
1258
            version="2.0" size="783643" />
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1259
    <dependencies/>
322 by Marcin Wojdyr
adding dependencies, patch for libffi
1260
    <after>
1261
      <dep package="python"/>
1262
    </after>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1263
  </distutils>
931 by Marcin Wojdyr
ccp4.xml: add --install-scripts=${prefix}/libexec for easyinstall, pip, bzr
1264
  <distutils id="pip" installargs="--install-scripts=${prefix}/libexec">
1300 by ccp4
update location of pypi branches
1265
    <branch repo="pypi" module="source/p/pip/pip-${version}.tar.gz"
993 by Marcin Wojdyr
ccp4.xml: updated pip, hopefully this will resolve some proxy issues
1266
            version="1.5.6" size="938120" />
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1267
    <dependencies/>
322 by Marcin Wojdyr
adding dependencies, patch for libffi
1268
    <after>
1269
      <dep package="python"/>
1270
    </after>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1271
  </distutils>
1272
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1273
  <distutils id="numpy">
1300 by ccp4
update location of pypi branches
1274
    <branch repo="pypi" module="a5/16/8a678404411842fe02d780b5f0a676ff4d79cd58f0f22acddab1b392e230/numpy-${version}.zip"
1257.1.1 by Tom Burnley
move to numpy 1.12.1
1275
            version="1.12.1">
1257.1.7 by Charles Ballard
activate numpy patch for intel compilers
1276
      <patch file="numpy-intelcompiler.patch" strip="0"/>
1137 by Charles Ballard
add patch for numpy distutils intel compiler on darwin
1277
    </branch>
754 by Marcin Wojdyr
add missing dependecies
1278
    <dependencies>
1257.1.5 by Tom Burnley
add setuptools dep for numpy
1279
      <dep package="setuptools"/>
754 by Marcin Wojdyr
add missing dependecies
1280
      <dep package="lapack"/>
1281
    </dependencies>
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1282
    <after>
1283
      <dep package="python"/>
1284
    </after>
1285
  </distutils>
1286
1118 by Marcin Wojdyr
add scipy
1287
  <distutils id="scipy">
1277 by Charles Ballard
set conditional for intel compiler and scipy
1288
    <if condition-set='intel'>
1289
      <buildargs value="--compiler=intelem --fcompiler=intelem" /> 
1290
    </if>
1300 by ccp4
update location of pypi branches
1291
    <branch repo="pypi" module="source/s/scipy/scipy-${version}.tar.gz"
1159 by Marcin Wojdyr
update numpy & scipy
1292
            version="0.16.1" size="12221561" />
1118 by Marcin Wojdyr
add scipy
1293
    <dependencies>
1294
      <dep package="numpy"/>
1295
    </dependencies>
1296
  </distutils>
1297
1175 by Marcin Wojdyr
add pandas
1298
  <distutils id="pandas">
1300 by ccp4
update location of pypi branches
1299
    <branch repo="pypi" module="source/p/pandas/pandas-${version}.tar.gz"
1175 by Marcin Wojdyr
add pandas
1300
            version="0.17.1" size="6674479" />
1301
    <dependencies>
1302
      <dep package="numpy"/>
1303
      <dep package="python-dateutil"/>
1177 by Marcin Wojdyr
adding pytz - required by pandas
1304
      <dep package="pytz"/>
1175 by Marcin Wojdyr
add pandas
1305
    </dependencies>
1306
  </distutils>
1307
967 by Marcin Wojdyr
ccp4.xml: added biopython
1308
  <distutils id="biopython">
1300 by ccp4
update location of pypi branches
1309
    <branch repo="pypi" module="source/b/biopython/biopython-${version}.tar.gz"
1102 by Marcin Wojdyr
updated biopython
1310
            version="1.65" size="12641382" />
967 by Marcin Wojdyr
ccp4.xml: added biopython
1311
    <dependencies>
1312
      <dep package="numpy"/>
1313
    </dependencies>
1314
  </distutils>
1315
1284 by Charles Ballard
try to merge in changes from series-71
1316
  <distutils id="docutils">
1300 by ccp4
update location of pypi branches
1317
    <branch repo="pypi" module="source/d/docutils/docutils-${version}.tar.gz"
1284 by Charles Ballard
try to merge in changes from series-71
1318
            version="0.12" size="1618353" />
1319
    <after>
1320
      <dep package="python"/>
1321
    </after>
1322
  </distutils>
1323
1324
<!--
1325
  <distutils id="ipython">
1326
    <branch repo="pypi" module="i/ipython/ipython-${version}.tar.gz"
1327
            version="2.1.0" size="3792998" />
1328
    <after>
1329
      <dep package="python"/>
1330
    </after>
1331
  </distutils>
1332
1333
  <distutils id="pyopengl">
1334
    <branch repo="pypi" module="p/pyopengl/PyOpenGL-${version}.tar.gz"
1335
            version="3.1.0" size="3792998" />
1336
    <after>
1337
      <dep package="python"/>
1338
    </after>
1339
  </distutils>
1340
1341
  <distutils id="numpydoc">
1342
    <branch repo="pypi" module="n/numpydoc/numpydoc-${version}.tar.gz"
1343
            version="0.5" size="3792998" />
1344
    <after>
1345
      <dep package="python"/>
1346
    </after>
1347
  </distutils>
1348
1349
  <distutils id="reportlab">
1350
    <branch repo="pypi" module="r/reportlab/reportlab-${version}.tar.gz"
1351
            version="2.6" size="3792998" />
1352
    <after>
1353
      <dep package="python"/>
1354
    </after>
1355
  </distutils>
1356
1357
  <distutils id="send2trash">
1358
    <branch repo="pypi" module="s/Send2Trash/Send2Trash-${version}.tar.gz"
1359
            version="1.3.0" size="3792998" />
1360
    <after>
1361
      <dep package="python"/>
1362
    </after>
1363
  </distutils>
1364
1365
  <distutils id="sphinx">
1366
    <branch repo="pypi" module="s/sphinx/Sphinx-${version}.tar.gz"
1367
            version="1.2.2" size="3792998" />
1368
    <dependencies>
1369
      <dep package="numpydoc"/>
1370
    </dependencies>
1371
    <after>
1372
      <dep package="python"/>
1373
    </after>
1374
  </distutils>
1375
-->
1376
1061 by Marcin Wojdyr
add PyCrypto (for arcimboldo)
1377
  <distutils id="pycrypto">
1300 by ccp4
update location of pypi branches
1378
    <branch repo="pypi" module="source/p/pycrypto/pycrypto-${version}.tar.gz"
1061 by Marcin Wojdyr
add PyCrypto (for arcimboldo)
1379
            version="2.6.1" size="446240" />
1130 by Marcin Wojdyr
pycrypto depends on gmp
1380
    <dependencies>
1381
      <dep package="gmp"/>
1382
    </dependencies>
1115 by Marcin Wojdyr
add paramiko (for arcimboldo)
1383
    <after>
1384
      <dep package="python"/>
1385
    </after>
1061 by Marcin Wojdyr
add PyCrypto (for arcimboldo)
1386
  </distutils>
1387
990 by Marcin Wojdyr
ccp4.xml: added pillow
1388
  <distutils id="pillow">
1300 by ccp4
update location of pypi branches
1389
    <branch repo="pypi" module="source/P/Pillow/Pillow-${version}.tar.gz"
990 by Marcin Wojdyr
ccp4.xml: added pillow
1390
            version="2.6.1" size="7321920" />
1391
    <dependencies>
1392
      <dep package="libjpeg"/>
1393
      <dep package="zlib"/>
1001 by Marcin Wojdyr
ccp4.xml fix wrong pillow dependency name
1394
      <dep package="tiff"/>
990 by Marcin Wojdyr
ccp4.xml: added pillow
1395
    </dependencies>
991 by Marcin Wojdyr
ccp4.xml: add setuptools to ccpem
1396
    <after>
1397
      <dep package="python"/>
1398
      <dep package="setuptools"/>
1399
    </after>
990 by Marcin Wojdyr
ccp4.xml: added pillow
1400
  </distutils>
1401
1115 by Marcin Wojdyr
add paramiko (for arcimboldo)
1402
  <distutils id="paramiko">
1300 by ccp4
update location of pypi branches
1403
    <branch repo="pypi" module="source/p/paramiko/paramiko-${version}.tar.gz"
1115 by Marcin Wojdyr
add paramiko (for arcimboldo)
1404
            version="1.15.2" size="1220578" />
1405
    <dependencies>
1406
      <dep package="pycrypto"/>
1407
    </dependencies>
1408
  </distutils>
1409
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1410
  <distutils id="python-dateutil">
1300 by ccp4
update location of pypi branches
1411
    <branch repo="pypi" module="source/p/python-dateutil/python-dateutil-2.4.2.tar.gz"
1175 by Marcin Wojdyr
add pandas
1412
            version="2.4.2" size="209120" />
1176 by Marcin Wojdyr
new python-dateutil depends on six
1413
    <dependencies>
1414
      <dep package="six"/>
1415
    </dependencies>
1416
    <after>
1417
      <dep package="python"/>
1418
      <dep package="setuptools"/>
1419
    </after>
1420
  </distutils>
1421
1177 by Marcin Wojdyr
adding pytz - required by pandas
1422
  <distutils id="pytz">
1300 by ccp4
update location of pypi branches
1423
    <branch repo="pypi" module="source/p/pytz/pytz-2015.7.tar.gz"
1177 by Marcin Wojdyr
adding pytz - required by pandas
1424
            version="2015.7" size="282002" />
1425
    <after>
1426
      <dep package="python"/>
1427
      <dep package="setuptools"/>
1428
    </after>
1429
  </distutils>
1430
1176 by Marcin Wojdyr
new python-dateutil depends on six
1431
  <distutils id="six">
1300 by ccp4
update location of pypi branches
1432
    <branch repo="pypi" module="source/s/six/six-1.10.0.tar.gz"
1176 by Marcin Wojdyr
new python-dateutil depends on six
1433
            version="1.10.0" size="29630" />
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1434
    <dependencies/>
1435
    <after>
1436
      <dep package="python"/>
1175 by Marcin Wojdyr
add pandas
1437
      <dep package="setuptools"/>
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1438
    </after>
1439
  </distutils>
1440
1441
  <distutils id="pyparsing">
1300 by ccp4
update location of pypi branches
1442
    <branch repo="pypi" module="source/p/pyparsing/pyparsing-2.0.1.tar.gz"
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1443
            version="2.0.1" size="1129563" />
1444
    <dependencies/>
1445
    <after>
1446
      <dep package="python"/>
1447
    </after>
1448
  </distutils>
1449
1450
  <distutils id="matplotlib">
916 by Marcin Wojdyr
downgrade matplotlib to avoid dependency on newer freetype2
1451
    <!-- matplotlib 1.4 requires freetype2 2.4+, on RHEL5 it's 2.2.1 -->
1300 by ccp4
update location of pypi branches
1452
    <branch repo="pypi" module="source/m/matplotlib/matplotlib-${version}.tar.gz"
1193 by Marcin Wojdyr
update matplotlib as it doesn't build with the current numpy version
1453
            version="1.4.3" size="50413837">
708 by Marcin Wojdyr
matplotlib: don't install tests and sample-data
1454
      <patch file="matplotlib-setup-cfg.patch" strip="0"/>
1455
    </branch>
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1456
    <dependencies>
1193 by Marcin Wojdyr
update matplotlib as it doesn't build with the current numpy version
1457
       <dep package="freetype2"/>
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1458
       <dep package="numpy"/>
1459
       <dep package="python-dateutil"/>
1460
       <dep package="pyparsing"/>
910 by Marcin Wojdyr
updated numpy and matplotlib
1461
       <dep package="libpng"/>
934 by Marcin Wojdyr
ccp4.xml: add pyqt4 as dep of matplotlib
1462
       <dep package="pyqt4"/>
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1463
    </dependencies>
1464
    <after>
1465
      <dep package="python"/>
1466
    </after>
1467
  </distutils>
1468
1199 by Marcin Wojdyr
add MarkupSafe for PANDDA
1469
  <distutils id="markupsafe">
1300 by ccp4
update location of pypi branches
1470
    <branch repo="pypi" module="source/M/MarkupSafe/MarkupSafe-0.23.tar.gz"
1199 by Marcin Wojdyr
add MarkupSafe for PANDDA
1471
            version="0.23" size="13416" />
1472
    <dependencies/>
1473
    <after>
1474
      <dep package="python"/>
1475
    </after>
1476
  </distutils>
1477
1170 by Marcin Wojdyr
add jinja2
1478
  <distutils id="jinja2">
1300 by ccp4
update location of pypi branches
1479
    <branch repo="pypi" module="source/J/Jinja2/Jinja2-2.8.tar.gz"
1170 by Marcin Wojdyr
add jinja2
1480
            version="2.8" size="357055" />
1284 by Charles Ballard
try to merge in changes from series-71
1481
    <dependencies>
1482
      <dep package="markupsafe"/>
1483
    </dependencies>
1484
    <after>
1485
      <dep package="python"/>
1257.1.8 by Charles Ballard
add setuptools-scm, which may be required to get around pip issues in installing pytest-xdist
1486
    </after>
1276 by ccp4
add setuptools-scm for pytest-xdist, ccpem dependency
1487
  </distutils>
1488
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1489
  <repository type="tarball" name="lp" href="https://launchpad.net/"/>
931 by Marcin Wojdyr
ccp4.xml: add --install-scripts=${prefix}/libexec for easyinstall, pip, bzr
1490
  <distutils id="bzr" installargs="--install-scripts=${prefix}/libexec">
487 by Marcin Wojdyr
ccp4.xml: updated bzr
1491
    <branch repo="lp" module="bzr/2.6/2.6.0/+download/bzr-2.6.0.tar.gz"
1492
            version="2.6.0" size="11301124" />
322 by Marcin Wojdyr
adding dependencies, patch for libffi
1493
    <after>
1494
      <dep package="python"/>
1495
    </after>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1496
  </distutils>
1497
1285 by Charles Ballard
update location and version of hdf5, synch requirement to dials 1.7.2
1498
  <repository type="tarball" name="hdf5" href="https://support.hdfgroup.org/ftp/"/>
1075 by Marcin Wojdyr
update hdf5
1499
  <cmake id="hdf5"
1284 by Charles Ballard
try to merge in changes from series-71
1500
      cmakeargs="-DBUILD_TESTING=OFF -DHDF5_BUILD_EXAMPLES=OFF -DHDF5_BUILD_TOOLS=OFF -DHDF5_BUILD_CPP_LIB=OFF -DHDF5_BUILD_HL_LIB=ON -DHDF5_INSTALL_DATA_DIR=share/hdf5 -DHDF5_INSTALL_CMAKE_DIR=share/cmake">
1020 by Marcin Wojdyr
ccp4.xml: use hopefully more permanent url for hdf5 download
1501
    <branch repo="hdf5"
1285 by Charles Ballard
update location and version of hdf5, synch requirement to dials 1.7.2
1502
            module="HDF5/releases/hdf5-1.10/hdf5-${version}/src/hdf5-${version}.tar.gz"
1314 by ccp4
add patch for hdf5 on mingw
1503
            version="1.10.0-patch1" size="14007792">
1504
      <patch file="hdf5-mingw.patch" strip="0" />
1505
    </branch>
942 by Marcin Wojdyr
ccp4.xml: added hdf5
1506
    <dependencies>
1507
      <dep package="zlib"/>
1508
    </dependencies>
962 by Marcin Wojdyr
ccp4.xml: change hdf5 build to cmake - the only way to build it on Windows
1509
  </cmake>
942 by Marcin Wojdyr
ccp4.xml: added hdf5
1510
1284 by Charles Ballard
try to merge in changes from series-71
1511
  <distutils id="cython">
1310 by Charles Ballard
try darwin conditional for cython
1512
    <if condition-set='darwin'>
1513
      <installargs value="--prefix=${prefix}/Frameworks/Python.Framework/Versions/2.7" />
1514
    </if>
1300 by ccp4
update location of pypi branches
1515
    <branch repo="pypi" module="10/32/21873ff231e069f860098b1602bb9e3ae2806d2f73ba661b5d806f200243/Cython-0.27.1.tar.gz"
1298 by Charles Ballard
update cython to 1.27 to compile h5py
1516
            version="0.27" size="1773306" checkoutdir="Cython-${version}" />
1284 by Charles Ballard
try to merge in changes from series-71
1517
  </distutils>
1518
1297 by Charles Ballard
update h5py to 2.7.1 for dials 1.7.2
1519
  <distutils id="h5py" buildargs="configure --hdf5=${prefix}/lib ">
1300 by ccp4
update location of pypi branches
1520
    <branch repo="pypi" module="41/7a/6048de44c62fc5e618178ef9888850c3773a9e4be249e5e673ebce0402ff/h5py-2.7.1.tar.gz"
1297 by Charles Ballard
update h5py to 2.7.1 for dials 1.7.2
1521
            version="2.7.1" size="264225">
1284 by Charles Ballard
try to merge in changes from series-71
1522
      <patch file="h5py-mingw.patch" strip="1" />
1297 by Charles Ballard
update h5py to 2.7.1 for dials 1.7.2
1523
      <patch file="h5py-shared.patch" strip="0" />
1284 by Charles Ballard
try to merge in changes from series-71
1524
    </branch>
942 by Marcin Wojdyr
ccp4.xml: added hdf5
1525
    <dependencies>
1284 by Charles Ballard
try to merge in changes from series-71
1526
      <dep package="cython"/>
942 by Marcin Wojdyr
ccp4.xml: added hdf5
1527
      <dep package="hdf5"/>
1528
      <dep package="numpy"/>
1529
    </dependencies>
1530
  </distutils>
1531
1139 by Andrey Lebedev
arcimboldo is now build from sources; added ecdsa module
1532
  <distutils id="ecdsa">
1300 by ccp4
update location of pypi branches
1533
    <branch repo="pypi" module="source/e/ecdsa/ecdsa-${version}.tar.gz"
1139 by Andrey Lebedev
arcimboldo is now build from sources; added ecdsa module
1534
            version="0.13" size="55579"/>
1535
    <dependencies/>
1536
  </distutils>
1537
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1538
  <repository type="tarball" name="xmlsoft.org" href="ftp://xmlsoft.org/"/>
1284 by Charles Ballard
try to merge in changes from series-71
1539
  <autotools id="libxml2" autogenargs="--without-python --without-threads --with-zlib --bindir=${prefix}/devbin"
1540
             autogen-sh="configure" >
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1541
    <pkg-config>libxml-2.0.pc</pkg-config>
407 by Marcin Wojdyr
updated libxml2 to 2.9.1
1542
    <branch module="libxml2/libxml2-${version}.tar.gz"
1339 by Charles Ballard
correct morda-mp download location
1543
            repo="xmlsoft.org" version="2.9.6" size="5469624"/>
405 by Marcin Wojdyr
ccp4.xml: add zlib dependency to libxml2 (it doesn't really build w/o zlib)
1544
    <dependencies>
1545
      <dep package="zlib"/>
1546
    </dependencies>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1547
  </autotools>
1339 by Charles Ballard
correct morda-mp download location
1548
696 by Marcin Wojdyr
ccp4.xml: libxslt on Windows comment
1549
  <!-- on Windows patched using: mingw32-libxslt-use-correct-mkdir.patch -->
613 by Marcin Wojdyr
ccp4.xml: added more ccp4mg dependencies: suds, lxml, libxslt,
1550
  <autotools id="libxslt" autogenargs="--without-python --without-crypto --bindir=${prefix}/devbin">
1551
    <pkg-config>libxslt.pc</pkg-config>
1552
    <branch module="libxml2/libxslt-${version}.tar.gz"
1553
            repo="xmlsoft.org" version="1.1.28" size="3435907"/>
1554
    <dependencies>
1555
      <dep package="libxml2"/>
1556
    </dependencies>
1557
  </autotools>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1558
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1559
  <repository type="tarball" name="gc"
717 by Marcin Wojdyr
ccp4.xml: gc download location changed, update gc-alpha to gc-7.2e
1560
              href="http://www.hboehm.info/gc/gc_source/"/>
132 by Marcin Wojdyr
updated moduleset
1561
  <autotools id="gc" autogen-sh="configure"
718 by Marcin Wojdyr
ccp4.xml: gc configure needs --enable-cplusplus for rapper (how did it work
1562
             autogenargs="--disable-threads --enable-cplusplus">
717 by Marcin Wojdyr
ccp4.xml: gc download location changed, update gc-alpha to gc-7.2e
1563
    <branch module="gc-7.2e.tar.gz"
1564
            repo="gc" version="7.2e" checkoutdir="gc-7.2e" size="1291186"/>
110 by Marcin Wojdyr
updated moduleset
1565
  </autotools>
1566
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1567
  <repository type="tarball" name="lapack_site"
1568
              href="http://www.netlib.org/lapack/"/>
1047 by Marcin Wojdyr
always call cmake with -DBUILD_SHARED_LIBS=...
1569
  <cmake id="lapack" cmakeargs="-DBUILD_TESTING=OFF">
711 by Marcin Wojdyr
ccp4.xml: build LAPACK as shared library for use in numpy (+ upgrade to 3.5.0)
1570
    <branch repo="lapack_site" version="3.5.0" module="lapack-${version}.tgz"
1571
            size="6313139"/>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1572
  </cmake>
1573
232 by Marcin Wojdyr
disable parallel building (make -jN) of FFTW2, it sometimes goes wrong
1574
  <!-- compile in-source, otherwise fftw.h in srcdir is not modified by
1575
       configure; since the source could be already built by different
1576
       compiler we run make clean first (and -j1 to prevent clean and make
1577
       running in parallel -->
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1578
  <repository type="tarball" name="fftw_site" href="http://www.fftw.org/"/>
774 by Marcin Wojdyr
ccp4.xml: build fftw2 with fortran support
1579
  <autotools id="fftw2" autogenargs="--enable-float"
329 by Marcin Wojdyr
ccp4.xml: added guile-gtk, guile-gui, oldssm
1580
             supports-non-srcdir-builds="no" makeargs="-j1 clean all">
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1581
    <branch repo="fftw_site" module="fftw-2.1.5.tar.gz"
889 by Charles Ballard
workaround for quotes in GLOB_options for ifc
1582
            version="2.1.5" size="1256888">
1583
      <patch file="fftw2-configure.patch" strip="0" />
1584
    </branch>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1585
  </autotools>
1586
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1587
  <repository type="tarball" name="jpeg" href="http://www.ijg.org/files/"/>
455 by Marcin Wojdyr
introduced directory devbin/ for binaries not needed after bulding is done
1588
  <autotools id="libjpeg" autogenargs="--bindir=${prefix}/devbin">
1095 by Marcin Wojdyr
update libjpeg and libtiff
1589
    <branch repo="jpeg" module="jpegsrc.v${version}.tar.gz" version="9a"
1590
            size="1000034" checkoutdir="jpeg-${version}"/>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1591
  </autotools>
1592
1284 by Charles Ballard
try to merge in changes from series-71
1593
  <autotools id="libpng" 
1594
             autogenargs="--bindir=${prefix}/devbin"
1266 by Charles Ballard
switch some autogen.sh runs to configure
1595
    autogen-sh="configure" >
320 by Marcin Wojdyr
more coot dependencies
1596
    <pkg-config>libpng.pc</pkg-config>
306 by Marcin Wojdyr
added more coot dependencies
1597
    <branch repo="sf" module="libpng/libpng-${version}.tar.gz"
1094 by Marcin Wojdyr
update libpng 1.6.12 -> 1.6.18
1598
            version="1.6.18" size="1400221"/>
306 by Marcin Wojdyr
added more coot dependencies
1599
    <dependencies>
1600
      <dep package="zlib"/>
1601
    </dependencies>
813 by Marcin Wojdyr
libpng: go back to autoconf & add patch to skip building programs
1602
  </autotools>
306 by Marcin Wojdyr
added more coot dependencies
1603
1272 by Charles Ballard
turn of regeneation of autotools in freeglut, autogen-sh=configure
1604
  <autotools id="freeglut" autogenargs="" 
1605
    autogen-sh="configure">
1055 by Marcin Wojdyr
reverted freeglut to 2.8.1 -- too many build problems with 3.0.0
1606
    <branch repo="sf" module="freeglut/freeglut-2.8.1.tar.gz"
1607
            version="2.8.1" size="1005343">
1608
      <patch file="freeglut-smooth_opengl3.patch" strip="0" />
1609
      <patch file="freeglut-strokechar.patch" strip="0" />
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
1610
    </branch>
339 by Marcin Wojdyr
added freeglut
1611
    <dependencies>
1612
    </dependencies>
1055 by Marcin Wojdyr
reverted freeglut to 2.8.1 -- too many build problems with 3.0.0
1613
  </autotools>
339 by Marcin Wojdyr
added freeglut
1614
372 by Marcin Wojdyr
ccp4.xml: add boost
1615
  <custom id="boost"
1245 by Charles Ballard
update RDKit to 2016_09_04
1616
          configure="./bootstrap.sh --with-libraries=serialization,regex,chrono,date_time,filesystem,iostreams,program_options,thread,system,python"
820 by Marcin Wojdyr
ccp4.xml: add -d+2 option (verbose output) to boost build
1617
          build="./b2 -q -d+2 -sNO_BZIP2=1 --layout=system variant=release link=shared linkflags=&quot;${LDFLAGS}&quot; stage"
1618
          install="./b2 -q -d+2 -sNO_BZIP2=1 --layout=system variant=release link=shared linkflags=&quot;${LDFLAGS}&quot; install --prefix=${dest}"
372 by Marcin Wojdyr
ccp4.xml: add boost
1619
          clean="./b2 --clean-all">
1182 by Marcin Wojdyr
downgrade boost to 1.59.0, because of:
1620
    <branch repo="sf" module="boost/boost/1.59.0/boost_1_59_0.tar.gz"
1621
            version="1.59.0" size="83709983">
1622
      <patch file="boost-make-setter.patch" strip="0" />
1623
    </branch>
393 by Marcin Wojdyr
ccp4.xml: boost depends on zlib and bzip2
1624
    <dependencies>
1625
      <dep package="zlib"/>
1626
    </dependencies>
372 by Marcin Wojdyr
ccp4.xml: add boost
1627
  </custom>
339 by Marcin Wojdyr
added freeglut
1628
1223 by Andrey Lebedev
changed url for libtiff
1629
  <repository type="tarball" name="tiff" href="http://download.osgeo.org/"/>
831 by Marcin Wojdyr
install libtiff and Pixie like other packages (libs in $CCP4/lib, etc)
1630
  <autotools id="tiff" autogenargs="--disable-lzma"
1266 by Charles Ballard
switch some autogen.sh runs to configure
1631
             autogen-sh="configure"
831 by Marcin Wojdyr
install libtiff and Pixie like other packages (libs in $CCP4/lib, etc)
1632
             makeargs="SUBDIRS='port libtiff'"
1633
             makeinstallargs="SUBDIRS='port libtiff' install">
1095 by Marcin Wojdyr
update libjpeg and libtiff
1634
   <branch repo="tiff" module="libtiff/tiff-${version}.tar.gz"
1635
            version="4.0.5" size="2135410"/>
831 by Marcin Wojdyr
install libtiff and Pixie like other packages (libs in $CCP4/lib, etc)
1636
   <pkg-config>libtiff-4.pc</pkg-config>
1637
   <dependencies>
1638
     <dep package="zlib"/>
1639
     <dep package="libjpeg"/>
1640
   </dependencies>
1641
  </autotools>
765 by Ville Uski
Apply Stuart's patches to compile pixie with ccp4mg, and tiff with pixie.
1642
1143 by Marcin Wojdyr
added patch for pixie with all flex/bison generated files
1643
  <!-- sdr files in the tarball have \r\n line endings and don't work on Unix,
831 by Marcin Wojdyr
install libtiff and Pixie like other packages (libs in $CCP4/lib, etc)
1644
       they are regenerated after installation (triggers/pixie.trigger).
1645
       $PIXIEHOME is respected only on OSX, on Linux $SHADERS and $DISPLAY
1646
       need to be set.
765 by Ville Uski
Apply Stuart's patches to compile pixie with ccp4mg, and tiff with pixie.
1647
  -->
831 by Marcin Wojdyr
install libtiff and Pixie like other packages (libs in $CCP4/lib, etc)
1648
  <autotools id="pixie"
1649
             autogenargs="--bindir=${prefix}/libexec --disable-selfcontained"
1650
             supports-non-srcdir-builds="no">
1651
    <branch repo="sf" module="pixie/Pixie-src-2.2.6.tgz"
1652
            checkoutdir="Pixie-2.2.6" version="2.2.6" size="9993504">
765 by Ville Uski
Apply Stuart's patches to compile pixie with ccp4mg, and tiff with pixie.
1653
      <patch file="pixie-2.2.6-zlib-1.2.5.2.patch" strip="0"/>
1143 by Marcin Wojdyr
added patch for pixie with all flex/bison generated files
1654
      <patch file="pixie-generated.patch" strip="0"/>
831 by Marcin Wojdyr
install libtiff and Pixie like other packages (libs in $CCP4/lib, etc)
1655
    </branch>
765 by Ville Uski
Apply Stuart's patches to compile pixie with ccp4mg, and tiff with pixie.
1656
    <dependencies>
1657
      <dep package="tiff"/>
1658
    </dependencies>
831 by Marcin Wojdyr
install libtiff and Pixie like other packages (libs in $CCP4/lib, etc)
1659
  </autotools>
765 by Ville Uski
Apply Stuart's patches to compile pixie with ccp4mg, and tiff with pixie.
1660
390 by Marcin Wojdyr
ccp4.xml: tweak qt4 build
1661
  <!--
1662
  on Linux qt4 compilation requires dev files for fontconfig and xrender
1663
  -->
374 by Marcin Wojdyr
ccp4.xml: added qt4
1664
  <repository type="tarball" name="qt4"
1096 by Marcin Wojdyr
update Qt to 4.8.7
1665
              href="http://download.qt.io/official_releases/qt/"/>
502 by Marcin Wojdyr
reordered Qt4 configure arguments
1666
  <!-- the first lines (before -release) are unix-specific -->
374 by Marcin Wojdyr
ccp4.xml: added qt4
1667
  <custom id="qt4"
476 by Marcin Wojdyr
ccp4.xml: use "devbin" as bindir for qt4
1668
   configure="${srcdir}/configure -prefix ${prefix} -bindir ${prefix}/devbin
623 by Marcin Wojdyr
ccp4.xml: fix to the last commit (-plugindir)
1669
   -plugindir ${libdir}/qt4/plugins
502 by Marcin Wojdyr
reordered Qt4 configure arguments
1670
   -no-sse3 -no-ssse3 -no-sse4.1 -no-sse4.2 -no-avx
1671
   -fontconfig -opengl -no-sm -no-xshape -no-xvideo
374 by Marcin Wojdyr
ccp4.xml: added qt4
1672
   -release -opensource -xmlpatterns
729 by Marcin Wojdyr
qt4: remove -no-sse2 option from 64-bit build
1673
   -no-3dnow -no-neon
1189 by Marcin Wojdyr
do not disable sqlite support in qt4
1674
   -no-qt3support -qt-libmng
564 by Marcin Wojdyr
ccp4.xml: remove -no-dbus from qt4 options -- due to strange errors on some
1675
   -no-phonon -no-phonon-backend -no-multimedia
374 by Marcin Wojdyr
ccp4.xml: added qt4
1676
   -no-audio-backend -webkit -no-declarative -no-declarative-debug
603 by Charles Ballard
QtWebkit fails to compile on OS X if QScript is not there, so remove -no-script
1677
   -no-scripttools
564 by Marcin Wojdyr
ccp4.xml: remove -no-dbus from qt4 options -- due to strange errors on some
1678
   -no-cups -no-openvg
374 by Marcin Wojdyr
ccp4.xml: added qt4
1679
   -no-s60 -nomake examples -nomake demos -nomake tools -confirm-license"
390 by Marcin Wojdyr
ccp4.xml: tweak qt4 build
1680
   build="${}" install="make INSTALL_ROOT=${destdir} install" clean="${}"
374 by Marcin Wojdyr
ccp4.xml: added qt4
1681
   supports-non-srcdir-builds="yes">
1096 by Marcin Wojdyr
update Qt to 4.8.7
1682
    <branch repo="qt4" version="4.8.7" size="241075567"
1683
            module="4.8/4.8.7/qt-everywhere-opensource-src-4.8.7.tar.gz"/>
374 by Marcin Wojdyr
ccp4.xml: added qt4
1684
    <dependencies>
1685
      <dep package="zlib"/>
1686
      <dep package="libpng"/>
1687
      <dep package="libjpeg"/>
1688
      <dep package="openssl"/>
859 by Marcin Wojdyr
ccp4.xml: build qt4 with mng and tiff support (requested for i2)
1689
      <dep package="tiff"/>
1189 by Marcin Wojdyr
do not disable sqlite support in qt4
1690
      <dep package="sqlite3"/>
374 by Marcin Wojdyr
ccp4.xml: added qt4
1691
    </dependencies>
980 by Marcin Wojdyr
ccp4.xml: note that qt4 may depend on glib (on Linux)
1692
    <after> <!-- on Linux it may use glib -->
1693
      <dep package="glib"/>
1694
    </after>
374 by Marcin Wojdyr
ccp4.xml: added qt4
1695
  </custom>
1696
976 by Marcin Wojdyr
ccp4.xml: pass LDFLAGS also to pyqt4
1697
  <custom id="sip" configure="python ${srcdir}/configure.py --bindir=${prefix}/devbin --destdir=${prefix}/lib/python2.7/site-packages --incdir=${prefix}/include --sipdir=${prefix}/share/sip LFLAGS+=&quot;${LDFLAGS}&quot;"
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1698
          build="${}" install="${}" clean="${}"
1699
          supports-non-srcdir-builds="no">
1700
    <branch repo="sf" module="pyqt/sip/sip-${version}/sip-${version}.tar.gz"
1101 by Marcin Wojdyr
update sip and pyqt4
1701
            version="4.16.9" size="957858"/>
617 by Marcin Wojdyr
ccp4.xml: sip: change dependency on Python to "after" Python (building
1702
    <after>
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1703
      <dep package="python"/>
617 by Marcin Wojdyr
ccp4.xml: sip: change dependency on Python to "after" Python (building
1704
    </after>
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1705
  </custom>
1706
1707
  <custom id="pyqt4"
1257.1.9 by Tom Burnley
add dssp dep to ccpem
1708
          configure="python ${srcdir}/configure.py --verbose --confirm-license --no-designer-plugin --no-qsci-api -e QtCore -e QtGui -e QtNetwork -e QtScript -e QtXml -e QtOpenGL -e QtSql -e QtSvg -e QtTest -e QtWebKit -e QtXmlPatterns --bindir=${prefix}/devbin --destdir=${prefix}/lib/python2.7/site-packages --sipdir=${prefix}/share/sip LFLAGS+=&quot;${LDFLAGS}&quot;"
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1709
          build="${}" install="${} INSTALL_ROOT=${destdir}" clean="${}"
1710
          supports-non-srcdir-builds="yes">
622 by Marcin Wojdyr
ccp4.xml: build qt4 with -plugindir ${libdir}/qt4
1711
    <!-- no real differences between PyQt-mac and PyQt-x11, only differences
1712
         in doc/html/ and in comments in sip/ -->
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1713
    <branch repo="sf"
1714
            module="pyqt/PyQt4/PyQt-${version}/PyQt-x11-gpl-${version}.tar.gz"
1101 by Marcin Wojdyr
update sip and pyqt4
1715
            version="4.11.4" size="11317088"/>
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1716
    <dependencies>
1717
      <dep package="sip"/>
735 by Marcin Wojdyr
ccp4.xml: pyqt4 4.10.3 -> 4.10.4 (should fix some build problems)
1718
    </dependencies>
1719
    <after>
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1720
      <dep package="qt4"/>
735 by Marcin Wojdyr
ccp4.xml: pyqt4 4.10.3 -> 4.10.4 (should fix some build problems)
1721
    </after>
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1722
  </custom>
1723
613 by Marcin Wojdyr
ccp4.xml: added more ccp4mg dependencies: suds, lxml, libxslt,
1724
  <distutils id="suds">
1300 by ccp4
update location of pypi branches
1725
    <branch repo="pypi" module="source/s/suds/suds-${version}.tar.gz"
613 by Marcin Wojdyr
ccp4.xml: added more ccp4mg dependencies: suds, lxml, libxslt,
1726
            version="0.4" size="104013"/>
1727
    <dependencies/>
1728
    <after>
1729
      <dep package="python"/>
1730
      <dep package="setuptools"/>
1731
    </after>
1732
  </distutils>
1733
1284 by Charles Ballard
try to merge in changes from series-71
1734
  <distutils id="psutil">
1300 by ccp4
update location of pypi branches
1735
    <branch repo="pypi" module="source/p/psutil/psutil-${version}.tar.gz"
1284 by Charles Ballard
try to merge in changes from series-71
1736
            version="3.2.2" size="253502"/>
1737
    <dependencies/>
1738
    <after>
1739
      <dep package="python"/>
1740
      <dep package="setuptools"/>
1741
    </after>
1742
  </distutils>
1743
613 by Marcin Wojdyr
ccp4.xml: added more ccp4mg dependencies: suds, lxml, libxslt,
1744
  <distutils id="lxml">
1339 by Charles Ballard
correct morda-mp download location
1745
    <branch repo="pypi" module="89/dc/ec07a5adf6afb02ad4f5f7e1f7e1a2fc0e3d88ce4fe233ed4b3dabd07cbd/lxml-${version}.tar.gz"
1746
            version="4.1.0" size="4247102"/>
613 by Marcin Wojdyr
ccp4.xml: added more ccp4mg dependencies: suds, lxml, libxslt,
1747
    <dependencies>
1748
      <dep package="libxml2"/>
1749
      <dep package="libxslt"/>
1750
    </dependencies>
1751
    <after>
1752
      <dep package="python"/>
1753
      <dep package="setuptools"/>
1754
    </after>
1755
  </distutils>
1756
349 by Marcin Wojdyr
added raster3d-cmake.patch
1757
  <repository type="tarball" name="raster3d"
1758
              href="http://skuld.bmsc.washington.edu/raster3d/"/>
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
1759
  <cmake id="raster3d">
949 by Marcin Wojdyr
updated raster3d
1760
    <branch repo="raster3d" module="Raster3D_${version}.tar.gz" version="3.0-3">
1290 by Charles Ballard
raster3d-cmake.patch strip level is wrong
1761
      <patch file="raster3d-cmake.patch" strip="0" />
349 by Marcin Wojdyr
added raster3d-cmake.patch
1762
    </branch>
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
1763
    <dependencies>
1764
      <dep package="libgd"/>
1765
    </dependencies>
1766
  </cmake>
1767
1342 by ccp4
add conditional for ucs4 and plplot CMAKE_INSTALL_LIBDIR
1768
  <cmake id="plplot" cmakeargs="-DENABLE_DYNDRIVERS=0 -DDEFAULT_NO_BINDINGS=1 -DHAVE_QHULL=0 -DWITH_CSA=0 -DDEFAULT_NO_DEVICES=1 -DPLD_png=1 -DCMAKE_INSTALL_LIBDIR=${prefix}/lib">
588 by Marcin Wojdyr
ccp4.xml: added plplot
1769
    <branch repo="sf"
1770
            module="plplot/plplot/${version}%20Source/plplot-${version}.tar.gz"
1054 by Marcin Wojdyr
update plplot to 5.11.0 (because of building problems on OSX Yosemite)
1771
            version="5.11.0" size="15892751">
773 by Marcin Wojdyr
ccp4.xml: use $CCP4 instead of $PLPLOT_HOME in plplot
1772
      <patch file="plplot-home-env.patch" strip="0" />
1773
    </branch>
588 by Marcin Wojdyr
ccp4.xml: added plplot
1774
    <dependencies>
1775
      <dep package="libgd"/>
1776
    </dependencies>
1777
  </cmake>
1778
966 by Marcin Wojdyr
add macapp
1779
  <cmake id="macapp">
1780
    <branch/>
1781
  </cmake>
1782
1284 by Charles Ballard
try to merge in changes from series-71
1783
  <autotools id="wxwidgets" autogenargs=" --enable-unicode --with-opengl --enable-sound --enable-graphics_ctx --disable-mediactrl --enable-display --enable-geometry --enable-debug_flag --enable-optimise --disable-debugreport --enable-uiactionsim --enable-monolithic ">
1784
    <if condition-set="darwin">
1785
      <autogenargs value=" --enable-unicode --with-osx_cocoa --with-opengl --enable-sound --enable-graphics_ctx --disable-mediactrl --enable-display --enable-geometry --enable-debug_flag --enable-optimise --disable-debugreport --enable-uiactionsim --enable-monolithic --disable-precomp-headers "/>
1786
    </if>
1787
    <branch repo="sf" module="wxpython/wxPython-src-${version}.tar.bz2"
1788
            version="3.0.2.0" size="58304944">
1789
       <patch file="wxpython-init.patch" strip="0" />
1790
       <patch file="wxpython-build.patch" strip="0" />
1791
       <patch file="wxPython-3.0.2.0-plot.patch" strip="1"/>
1792
      </branch>
1793
  </autotools>
1794
1795
  <custom id="wxpython"
1796
          build="python ${srcdir}/wxPython/build-wxpython.py  --prefix=${prefix} --wxpy_installdir=${prefix} --installdir=${prefix} --no_wxbuild "
1797
          install="python ${srcdir}/wxPython/build-wxpython.py --prefix=${prefix} --install --no_wxbuild " clean="python ${srcdir}/build-wxpython.py --clean"
1798
          supports-non-srcdir-builds="no">
1799
    <if condition-set="darwin">
1800
      <build value="python ${srcdir}/wxPython/build-wxpython.py  --prefix=${prefix} --wxpy_installdir=${prefix} --installdir=${prefix} --no_wxbuild --osx_cocoa " />
1801
      <install value="python ${srcdir}/wxPython/build-wxpython.py --prefix=${prefix} --install --no_wxbuild " clean="python ${srcdir}/build-wxpython.py --osx_cocoa --clean " />
1802
    </if>
1803
    <branch repo="sf" module="wxpython/wxPython-src-${version}.tar.bz2"
1804
            version="3.0.2.0" size="58304944">
1805
       <patch file="wxpython-init.patch" strip="0" />
1806
       <patch file="wxpython-build.patch" strip="0" />
1807
       <patch file="wxPython-3.0.2.0-plot.patch" strip="1"/>
1808
      </branch>
1809
    <dependencies>
1810
      <dep package="wxwidgets"/>
1811
    </dependencies>
1812
  </custom>
1049 by Marcin Wojdyr
ccp4.xml: add longbow for ccpem
1813
1076 by Marcin Wojdyr
added probe and reduce from github.com/rlabduke
1814
  <cmake id="probe">
1815
    <branch repo="github-zip"
1816
        module="rlabduke/probe/archive/${version}.zip"
1817
        version="acc7f517c3e3830b2489f71cbc53049399f86909"
1818
        checkoutdir="probe-${version}">
1819
      <patch file="probe-cmake.patch" strip="0" />
1820
    </branch>
1821
  </cmake>
1822
1823
  <cmake id="reduce">
1824
    <branch repo="github-zip"
1825
        module="rlabduke/reduce/archive/${version}.zip"
1826
        version="9fb41bbc04a2b611832231fcfc7ab8f670083bef"
1827
        checkoutdir="reduce-${version}">
1828
      <patch file="reduce-cmake.patch" strip="0" />
1829
    </branch>
1830
  </cmake>
1831
1139 by Andrey Lebedev
arcimboldo is now build from sources; added ecdsa module
1832
<!--
1121 by Marcin Wojdyr
add arcimboldo
1833
  <custom id="arcimboldo" install_to="bin/* bin/, arcimboldo lib/py2/">
1834
    <branch repo="files" version="3.0.1-test1"
1835
            module="arcimboldo-${version}.tar.gz"/>
1139 by Andrey Lebedev
arcimboldo is now build from sources; added ecdsa module
1836
-->
1837
  <cmake id="arcimboldo">
1838
    <branch/>
1121 by Marcin Wojdyr
add arcimboldo
1839
    <dependencies>
1840
      <dep package="scipy"/>
1841
      <dep package="biopython"/>
1842
      <dep package="matplotlib"/>
1843
      <dep package="paramiko"/>
1139 by Andrey Lebedev
arcimboldo is now build from sources; added ecdsa module
1844
      <dep package="ecdsa"/>
1284 by Charles Ballard
try to merge in changes from series-71
1845
      <dep package="python-igraph"/>
1846
      <dep package="progressbar"/>
1847
      <dep package="scikit-learn"/>
1121 by Marcin Wojdyr
add arcimboldo
1848
    </dependencies>
1139 by Andrey Lebedev
arcimboldo is now build from sources; added ecdsa module
1849
  </cmake>
1121 by Marcin Wojdyr
add arcimboldo
1850
1257.1.25 by Andrey Lebedev
added morda-mp
1851
  <cmake id="morda-mp">
1339 by Charles Ballard
correct morda-mp download location
1852
    <branch repo="oisin"/>
1329 by Charles Ballard
update morda-mp stub
1853
    <dependencies>
1854
    <dep package="psutil"/>
1855
    </dependencies>
1257.1.25 by Andrey Lebedev
added morda-mp
1856
  </cmake>
1857
1284 by Charles Ballard
try to merge in changes from series-71
1858
  <distutils id="python-igraph">
1859
    <branch repo="pypi" version="0.7.1.post6" size="377298"
1300 by ccp4
update location of pypi branches
1860
     module="0f/a0/4e7134f803737aa6eebb4e5250565ace0e2599659e22be7f7eba520ff017/python-igraph-0.7.1.post6.tar.gz"/>
1284 by Charles Ballard
try to merge in changes from series-71
1861
    <dependencies>
1862
      <!--<dep package="igraph"/> -->
1863
    </dependencies>
1864
    <after>
1865
      <dep package="python"/>
1866
      <dep package="setuptools"/>
1867
    </after>
1868
  </distutils>
1869
1870
  <distutils id="progressbar">
1871
    <branch repo="pypi" version="3.10.1" size="24090"
1300 by ccp4
update location of pypi branches
1872
            module="1c/de/a2f5feaf4048c941070e06e5814cb2adad73cdf47778920cb6c762145f17/progressbar2-3.10.1.tar.gz"/>
1284 by Charles Ballard
try to merge in changes from series-71
1873
    <dependencies>
1874
      <dep package="pytest-runner"/>
1875
      <dep package="python-utils"/>
1876
    </dependencies>
1877
    <after>
1878
      <dep package="python"/>
1879
      <dep package="setuptools"/>
1880
    </after>
1881
  </distutils>
1882
1883
  <distutils id="pytest-runner">
1884
    <branch repo="pypi" version="2.8" size="8535"
1300 by ccp4
update location of pypi branches
1885
            module="46/6c/ff61a9e0d513222afa3529bdb565a465812b7e50b218a5afd705f46b258c/pytest-runner-2.8.tar.gz"/>
1284 by Charles Ballard
try to merge in changes from series-71
1886
    <dependencies>
1887
      <dep package="setuptools-scm"/>
1888
    </dependencies>
1889
    <after>
1890
      <dep package="python"/>
1891
      <dep package="setuptools"/>
1892
    </after>
1893
  </distutils>
1894
1895
  <distutils id="python-utils">
1896
    <branch repo="pypi" version="2.0.0" size="5525"
1300 by ccp4
update location of pypi branches
1897
            module="24/f6/26474b0b52335864cf43a969987b7ab27ee14331def6ec82cbb8263bc937/python-utils-2.0.0.tar.gz"/>
1284 by Charles Ballard
try to merge in changes from series-71
1898
    <after>
1899
      <dep package="python"/>
1900
      <dep package="setuptools"/>
1901
    </after>
1902
  </distutils>
1903
1904
  <distutils id="setuptools-scm">
1905
    <branch repo="pypi" version="1.15.0" size="23677"
1300 by ccp4
update location of pypi branches
1906
            module="80/b7/31b6ae5fcb188e37f7e31abe75f9be90490a5456a72860fa6e643f8a3cbc/setuptools_scm-1.15.0.tar.gz"/>
1284 by Charles Ballard
try to merge in changes from series-71
1907
    <after>
1908
      <dep package="python"/>
1909
      <dep package="setuptools"/>
1910
    </after>
1911
  </distutils>
1912
1913
  <distutils id="scikit-learn">
1914
    <branch repo="pypi" version="0.17.1" size="7898571"
1300 by ccp4
update location of pypi branches
1915
            module="0d/1d/9c775f9403565f68aa23f9cef76c817a7115abd7ca1e1c5958a68c49fb6f/scikit-learn-0.17.1.tar.gz"/>
1284 by Charles Ballard
try to merge in changes from series-71
1916
    <dependencies>
1917
      <dep package="scipy"/>
1918
      <dep package="numpy"/>
1919
    </dependencies>
1920
    <after>
1921
      <dep package="python"/>
1922
      <dep package="setuptools"/>
1923
    </after>
1924
  </distutils>
1925
1325 by Charles Ballard
add auspex stub
1926
  <cmake id="auspex">
1927
    <branch/>
1928
    <dependencies>
1929
      <dep package="numpy"/>
1930
      <dep package="matplotlib"/>
1931
      <dep package="swig"/>
1932
      <dep package="clipper"/>
1933
    </dependencies>
1934
    <after>
1935
      <dep package="python"/>
1936
    </after>
1937
  </cmake>
1938
1225 by Marcin Wojdyr
add panddas (Unix-only for now)
1939
  <distutils id="panddas" buildargs="--for-ccp4">
1323 by Charles Ballard
update panddas to 0.2.11
1940
    <branch repo="pypi" version="0.2.11" size="4236160"
1343 by ccp4
wrong location for panddas source code
1941
            module="66/11/cb5cca9dfd07aab3e08a203044518566a8236763432bbd36ef3e1b880b82/panddas-0.2.11.tar.gz"/>
1175 by Marcin Wojdyr
add pandas
1942
    <dependencies>
1943
      <dep package="pandas"/>
1944
      <dep package="scipy"/>
1199 by Marcin Wojdyr
add MarkupSafe for PANDDA
1945
      <dep package="markupsafe"/>
1175 by Marcin Wojdyr
add pandas
1946
      <dep package="jinja2"/>
1947
    </dependencies>
1225 by Marcin Wojdyr
add panddas (Unix-only for now)
1948
  </distutils>
1175 by Marcin Wojdyr
add pandas
1949
1326 by Charles Ballard
update installation of dials-gui to try and workaround jhbuild issues
1950
  <distutils id="dials-gui" installargs="--install-platlib ${prefix}/lib/py2/site-packages --install-data ${prefix}/lib/py2/site-packages ">
1324 by Charles Ballard
add dials gui stub
1951
    <branch/>
1952
    <after>
1953
      <dep package="python"/>
1954
    </after>
1955
  </distutils>
1956
1284 by Charles Ballard
try to merge in changes from series-71
1957
  <distutils id="conkit"
1958
    buildargs="--script-python-path ccp4-python"
1959
    installargs="--install-scripts ${prefix}/bin --install-lib ${prefix}/lib/py2/site-packages ">
1960
      <branch repo="github-zip"
1289 by Charles Ballard
update simbad requirements
1961
          version="0.8.3"
1284 by Charles Ballard
try to merge in changes from series-71
1962
          module="rigdenlab/conkit/archive/${version}.zip"
1289 by Charles Ballard
update simbad requirements
1963
          checkoutdir="conkit-${version}">
1964
      </branch>
1284 by Charles Ballard
try to merge in changes from series-71
1965
    <dependencies>
1966
      <dep package="numpy"/>
1967
      <dep package="biopython"/>
1968
      <dep package="matplotlib"/>
1969
      <dep package="scipy"/>
1970
    </dependencies>
1971
    <after>
1972
      <dep package="python"/>
1973
      <dep package="setuptools"/>
1974
    </after>
1975
  </distutils>
1976
1977
  <distutils id="pyjob"
1978
    installargs="--install-scripts ${prefix}/bin --install-lib ${prefix}/lib/py2/site-packages ">
1979
      <branch repo="github-zip"
1320 by Charles Ballard
updates for simbad
1980
          version="0.1.5"
1284 by Charles Ballard
try to merge in changes from series-71
1981
          module="fsimkovic/pyjob/archive/${version}.zip"
1982
          checkoutdir="pyjob-${version}">
1983
      </branch>
1984
    <dependencies>
1985
      <dep package="numpy"/>
1986
    </dependencies>
1987
    <after>
1988
      <dep package="python"/>
1989
      <dep package="setuptools"/>
1990
    </after>
1991
  </distutils>
1992
1289 by Charles Ballard
update simbad requirements
1993
  <cmake id="simbad">
1994
    <branch repo="github-zip"
1328 by Charles Ballard
update simbad version to 0.1.6
1995
            version="0.1.6"
1289 by Charles Ballard
update simbad requirements
1996
            module="rigdenlab/simbad/archive/${version}.zip"
1997
            checkoutdir="simbad-${version}">
1998
    </branch>
1284 by Charles Ballard
try to merge in changes from series-71
1999
    <dependencies>
2000
      <dep package="numpy"/>
2001
      <dep package="pandas"/>
2002
      <dep package="pyjob"/>
1320 by Charles Ballard
updates for simbad
2003
      <dep package="amore-rs"/>
1284 by Charles Ballard
try to merge in changes from series-71
2004
    </dependencies>
1289 by Charles Ballard
update simbad requirements
2005
  </cmake>
1284 by Charles Ballard
try to merge in changes from series-71
2006
2007
  <repository type="tarball" name="igraph.org" href="http://igraph.org"/>
2008
  <autotools id="igraph">
2009
   <branch module="nightly/get/c/igraph-${version}.tar.gz"
2010
            repo="igraph.org" version="0.7.1" size="2967134"/>
2011
    <dependencies>
2012
      <dep package="libxml2"/>
2013
    </dependencies>
2014
  </autotools>
2015
1142 by Andrey Lebedev
added lorestr
2016
  <cmake id="lorestr">
2017
    <branch/>
2018
    <dependencies />
2019
  </cmake>
2020
1251 by Andrey Lebedev
added pdb deposition
2021
  <cmake id="pdbdeposition">
2022
    <branch/>
2023
    <dependencies />
2024
  </cmake>
2025
1284 by Charles Ballard
try to merge in changes from series-71
2026
  <cmake id="hdf5_lz4">
2027
     <branch repo="files" module="hdf5_lz4.tar.gz"
2028
            size="59270" version="0.2.0">
2029
        <patch file="hdf5-lz4-cmake.patch" strip="0" />
2030
     </branch>
2031
     <dependencies>
2032
        <dep package="hdf5"/>
2033
     </dependencies>
2034
  </cmake>
2035
2036
  <distutils id="bitshuffle" buildargs=" build_ext --omp 0 --hdf5dir=${prefix}" installargs=" --prefix=${prefix} --h5plugin --h5plugin-dir=${prefix}/lib/py2/base/lib">
2037
    <branch repo="files" module="bitshuffle.tar.gz"
2038
            size="103536" version="0.2.3">
2039
        <patch file="bitshuffle-mingw.patch" strip="1" />
2040
    </branch>
2041
    <dependencies>
2042
        <dep package="hdf5"/>
2043
    </dependencies>
2044
    <after>
2045
      <dep package="python"/>
2046
    </after>
2047
  </distutils>
2048
1338 by Charles Ballard
do not use needle
2049
<!--  <repository type="tarball" name="science-annex" href="http://science-annex.org/"/>
1284 by Charles Ballard
try to merge in changes from series-71
2050
  <autotools id="needle" 
2051
             supports-non-srcdir-builds="no">
2052
   <branch repo="science-annex" module="pub/emboss/EMBOSS-${version}.tar.gz"
2053
            version="6.6.0" size="117962028">
2054
      <patch file="emboss-makefile.patch" strip="1" />
2055
   </branch>
1338 by Charles Ballard
do not use needle
2056
  </autotools> -->
1284 by Charles Ballard
try to merge in changes from series-71
2057
49 by Marcin Wojdyr
added shared/static static options to autogenargs,
2058
  <metamodule id="default">
1 by Marcin Wojdyr
initial revision of jhbuild config
2059
    <dependencies>
957 by Marcin Wojdyr
updates for ccp4-core -> ccp4-base, ... transition
2060
      <dep package="ccp4-base"/>
2061
      <dep package="ccp4-lib-data"/>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
2062
      <dep package="mmdb2"/>
1 by Marcin Wojdyr
initial revision of jhbuild config
2063
      <dep package="ccif"/>
177 by Marcin Wojdyr
updated moduleset
2064
      <dep package="libccp4"/>
1 by Marcin Wojdyr
initial revision of jhbuild config
2065
      <dep package="ssm"/>
2066
      <dep package="ccp4srs"/>
47 by Marcin Wojdyr
updated modules list (not tested)
2067
      <dep package="gesamt"/>
177 by Marcin Wojdyr
updated moduleset
2068
      <dep package="molrep"/>
219 by Marcin Wojdyr
updated moduleset to add new bzr modules
2069
      <dep package="sfcheck"/>
2070
      <dep package="procheck"/>
2071
      <dep package="scala"/>
2072
      <dep package="dm21"/>
7 by Marcin Wojdyr
added refmac
2073
      <dep package="refmac"/>
190 by Marcin Wojdyr
moduleset changes: new LAPACK, refmac_dictionary is now in bazaar
2074
      <dep package="monomers"/>
15 by Marcin Wojdyr
added ccp4 from CVS (with cmake) to ccp4.modules
2075
      <dep package="ccp4-progs"/>
31 by Marcin Wojdyr
ccp4-jhbuild: added ccp4i to ccp4-all
2076
      <dep package="ccp4i"/>
219 by Marcin Wojdyr
updated moduleset to add new bzr modules
2077
      <dep package="imosflm"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
2078
      <dep package="clipper"/>
2079
      <dep package="pointless"/>
2080
      <dep package="aimless"/>
670 by Charles Ballard
trunk gets feckless build
2081
      <dep package="feckless"/>
56 by Marcin Wojdyr
a few small updates
2082
      <dep package="clipper-progs"/>
192 by Marcin Wojdyr
cprodrg is now in bzr, CVS no longer needed
2083
      <dep package="cprodrg"/>
79 by Marcin Wojdyr
ccp4.xml: added prosmart and updated ccp4-progs
2084
      <dep package="prosmart"/>
686 by Marcin Wojdyr
ccp4.xml: added crank2
2085
      <dep package="crank2"/>
177 by Marcin Wojdyr
updated moduleset
2086
      <dep package="examples"/>
2087
      <dep package="documentation"/>
365 by Marcin Wojdyr
minor tweaks
2088
      <dep package="ccp4dispatchers"/>
279 by Marcin Wojdyr
moduleset: added edstats
2089
      <dep package="edstats"/>
284 by Marcin Wojdyr
moduleset: added dimple to default set of packages
2090
      <dep package="dimple"/>
316 by Marcin Wojdyr
ccp4.xml: added tgutils to "all"
2091
      <dep package="mrbump"/>
2092
      <dep package="tgutils"/>
647 by ronan.keegan at ac
added spicker build
2093
      <dep package="spicker"/>
744 by ronan.keegan at ac
added prelyscar to 'all' option
2094
      <dep package="prelyscar"/>
652 by ronan.keegan at ac
Added theseus 2.0.6 to the build
2095
      <dep package="theseus"/>
177 by Marcin Wojdyr
updated moduleset
2096
      <!-- may depend on Tcl -->
101 by Marcin Wojdyr
updated ccp4-jhbuild
2097
      <dep package="diff-image"/>
122 by Marcin Wojdyr
added ccp4mapwish module
2098
      <dep package="ccp4mapwish"/>
188 by Marcin Wojdyr
jligand is now in bazaar
2099
      <!-- requires javac -->
2100
      <dep package="jligand"/>
177 by Marcin Wojdyr
updated moduleset
2101
      <!-- pulls libxml, gc -->
47 by Marcin Wojdyr
updated modules list (not tested)
2102
      <dep package="rapper"/>
177 by Marcin Wojdyr
updated moduleset
2103
      <!-- requires Qt, OpenGL -->
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
2104
      <dep package="pisa"/>
177 by Marcin Wojdyr
updated moduleset
2105
      <dep package="viewhkl"/>
220 by Marcin Wojdyr
added qtrview
2106
      <dep package="qtrview"/>
242 by Marcin Wojdyr
updated README and ccp4.xml
2107
      <!-- for now Ample is tested/working only on Unix -->
1284 by Charles Ballard
try to merge in changes from series-71
2108
      <dep package="conkit"/>
242 by Marcin Wojdyr
updated README and ccp4.xml
2109
      <dep package="ample"/>
365 by Marcin Wojdyr
minor tweaks
2110
      <dep package="raster3d"/>
1119 by Marcin Wojdyr
ccp4.xml: replace dssp with xssp in "default"
2111
      <dep package="xssp"/>
627 by Marcin Wojdyr
ccp4.xml: add blend
2112
      <dep package="blend"/>
827 by Marcin Wojdyr
ccp4.xml: add acedrg to "all"
2113
      <dep package="acedrg"/>
906 by Marcin Wojdyr
ccp4.xml: add libg
2114
      <dep package="libg"/>
875 by Marcin Wojdyr
ccp4.xml: add privateer to "all"
2115
      <dep package="privateer"/>
915 by Marcin Wojdyr
ccp4.xml: move biosequence tools from "ccp4-linux" to "default"
2116
      <dep package="clustalw2"/>
2117
      <dep package="mafft"/>
2118
      <dep package="hmmer"/>
1023 by Marcin Wojdyr
modified dependecies: added ccp4mg to "default", pixie and matplotlib to ccp4mg,
2119
      <dep package="ccp4mg"/>
1012 by Marcin Wojdyr
add biopython to "all", for ccp4i2
2120
      <dep package="biopython"/>
1023 by Marcin Wojdyr
modified dependecies: added ccp4mg to "default", pixie and matplotlib to ccp4mg,
2121
      <dep package="jsrview"/>
1065 by Marcin Wojdyr
add clipper-python and ccp4srs-python to the build
2122
      <dep package="clipper-python"/>
2123
      <dep package="ccp4srs-python"/>
1284 by Charles Ballard
try to merge in changes from series-71
2124
      <dep package="ccp4i2"/>
1077 by Marcin Wojdyr
ccp4.xml: add probe and reduce to "default"
2125
      <dep package="probe"/>
2126
      <dep package="reduce"/>
1284 by Charles Ballard
try to merge in changes from series-71
2127
      <dep package="balbes-pipeline"/>
2128
      <dep package="whatcheck"/>
1251 by Andrey Lebedev
added pdb deposition
2129
      <dep package="pdbdeposition"/>
1284 by Charles Ballard
try to merge in changes from series-71
2130
      <dep package="lorestr"/>
1344 by Charles Ballard
add auspex and dials-gui to default build
2131
      <dep package="auspex"/>
2132
      <dep package="dials-gui"/>
55 by Marcin Wojdyr
fixed module syntax
2133
    </dependencies>
1 by Marcin Wojdyr
initial revision of jhbuild config
2134
  </metamodule>
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
2135
445 by Marcin Wojdyr
replaced ccp4-unix with ccp4-osx and ccp4-linux
2136
  <metamodule id="ccp4-linux"> <!-- for Linux binaries  -->
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
2137
    <dependencies>
914 by Marcin Wojdyr
ccp4.xml: removed metamodule "all" (too many metamodules)
2138
      <dep package="default"/>
687 by Marcin Wojdyr
ccp4.xml: build tcltk84 on Linux by default
2139
      <dep package="tcltk84"/>
277 by Marcin Wojdyr
added hklview and a few other modules
2140
      <dep package="hklview"/>
399 by Marcin Wojdyr
added mosflm
2141
      <dep package="rotgen"/>
2142
      <dep package="mosflm"/>
925 by Marcin Wojdyr
ccp4.xml: build chooch on Unix
2143
      <dep package="chooch"/>
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
2144
      <dep package="pdb-extract"/>
1284 by Charles Ballard
try to merge in changes from series-71
2145
      <dep package="panddas"/>
1336 by Charles Ballard
arcimboldo on osx and linux only
2146
      <dep package="lorestr"/>
1257.1.25 by Andrey Lebedev
added morda-mp
2147
      <dep package="morda-mp"/>
1327 by Charles Ballard
reorganise location of simbad build
2148
      <dep package="simbad"/>
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
2149
    </dependencies>
2150
  </metamodule>
370 by Marcin Wojdyr
added all-sources metamodule to ccp4.xml and updated README
2151
445 by Marcin Wojdyr
replaced ccp4-unix with ccp4-osx and ccp4-linux
2152
  <metamodule id="ccp4-osx"> <!-- for OSX binaries  -->
2153
    <dependencies>
2154
      <dep package="pkgconf"/>
2155
      <dep package="freetype2"/>
1041 by Marcin Wojdyr
bootstrap patchelf on Linux
2156
      <dep package="default"/>
2157
      <dep package="tcltk84"/>
2158
      <dep package="hklview"/>
2159
      <dep package="rotgen"/>
2160
      <dep package="mosflm"/>
2161
      <dep package="chooch"/>
2162
      <dep package="pdb-extract"/>
1284 by Charles Ballard
try to merge in changes from series-71
2163
      <dep package="panddas"/>
1336 by Charles Ballard
arcimboldo on osx and linux only
2164
      <dep package="lorestr"/>
1257.1.25 by Andrey Lebedev
added morda-mp
2165
      <dep package="morda-mp"/>
1327 by Charles Ballard
reorganise location of simbad build
2166
      <dep package="simbad"/>
445 by Marcin Wojdyr
replaced ccp4-unix with ccp4-osx and ccp4-linux
2167
    </dependencies>
2168
  </metamodule>
2169
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
2170
  <metamodule id="coot-osx"> <!-- extra for coot on os x -->
2171
    <dependencies>
2172
      <dep package="pkgconf"/>
2173
      <dep package="freetype2"/>
843 by Charles Ballard
add coot8-osx target and bring coot-osx more uptodate
2174
      <dep package="intltool"/>
2175
      <!--<dep package="gettext"/>-->
2176
      <!--<dep package="fontconfig"/>-->
2177
      <!--<dep package="readline"/>-->
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
2178
      <dep package="coot"/>
2179
    </dependencies>
843 by Charles Ballard
add coot8-osx target and bring coot-osx more uptodate
2180
    <after>
2181
      <dep package="python"/>
2182
    </after>
2183
  </metamodule>
2184
445 by Marcin Wojdyr
replaced ccp4-unix with ccp4-osx and ccp4-linux
2185
  <metamodule id="ccp4-windows"> <!-- for Windows -->
371 by Marcin Wojdyr
changes for source bundles
2186
    <dependencies>
403 by Marcin Wojdyr
ccp4.xml: add pkgconf to ccp4-windows
2187
      <dep package="pkgconf"/>
495 by Marcin Wojdyr
ccp4.xml: build libgnurx by default on Windows
2188
      <dep package="libgnurx"/>
371 by Marcin Wojdyr
changes for source bundles
2189
      <dep package="freetype2"/>
914 by Marcin Wojdyr
ccp4.xml: removed metamodule "all" (too many metamodules)
2190
      <dep package="default"/>
371 by Marcin Wojdyr
changes for source bundles
2191
    </dependencies>
2192
  </metamodule>
2193
969 by Marcin Wojdyr
ccp4.xml: added balbesdb and metamodule balbes
2194
  <metamodule id="balbes">
2195
    <dependencies>
2196
      <dep package="balbes-pipeline"/>
2197
      <dep package="balbesdb"/>
2198
    </dependencies>
2199
  </metamodule>
2200
370 by Marcin Wojdyr
added all-sources metamodule to ccp4.xml and updated README
2201
  <metamodule id="all-sources"> <!-- sources for ccp4 source bundle -->
2202
    <dependencies>
445 by Marcin Wojdyr
replaced ccp4-unix with ccp4-osx and ccp4-linux
2203
      <dep package="ccp4-linux"/>
674 by Marcin Wojdyr
ccp4.xml: add dssp to all, libgnurx to all-sources
2204
      <dep package="ccp4-windows"/>
2205
      <dep package="ccp4-osx"/>
370 by Marcin Wojdyr
added all-sources metamodule to ccp4.xml and updated README
2206
      <dep package="ccp4-deprecated"/>
2207
      <!-- <dep package="setup"/> -->
2208
      <dep package="devtools"/>
2209
      <dep package="python"/>
2210
      <dep package="setuptools"/>
2211
      <dep package="pip"/>
1284 by Charles Ballard
try to merge in changes from series-71
2212
      <dep package="pillow"/>
2213
      <dep package="wxwidgets"/>
370 by Marcin Wojdyr
added all-sources metamodule to ccp4.xml and updated README
2214
      <dep package="bzr"/>
2215
      <dep package="cmake"/>
1023 by Marcin Wojdyr
modified dependecies: added ccp4mg to "default", pixie and matplotlib to ccp4mg,
2216
      <dep package="coot"/>
1133 by Marcin Wojdyr
ccp4.xml: add patchelf to all-sources
2217
      <dep package="patchelf"/>
370 by Marcin Wojdyr
added all-sources metamodule to ccp4.xml and updated README
2218
    </dependencies>
2219
  </metamodule>
371 by Marcin Wojdyr
changes for source bundles
2220
1284 by Charles Ballard
try to merge in changes from series-71
2221
  <!-- ccpem specific -->
2222
2223
  <custom id="modeller" install_to="* lib/modeller/">
2224
    <branch repo="files" module="https://salilab.org/modeller/9.19/modeller-9.19.tar.gz"
2225
            version="9.19"/>
2226
  </custom>
2227
2228
  <distutils id="py">
1300 by ccp4
update location of pypi branches
2229
    <branch repo="pypi" module="68/35/58572278f1c097b403879c1e9369069633d1cbad5239b9057944bb764782/py-1.4.34.tar.gz"
1284 by Charles Ballard
try to merge in changes from series-71
2230
            version="1.4.34"/>
2231
    <dependencies/>
2232
    <after>
2233
      <dep package="python"/>
2234
    </after>
2235
  </distutils>
2236
2237
  <distutils id="pytest">
1300 by ccp4
update location of pypi branches
2238
    <branch repo="pypi" module="15/c8/6b42bf58f91d72416806472512bb67dabc6edb5a6a8ace29853ff940400a/pytest-3.1.3.tar.gz"
1284 by Charles Ballard
try to merge in changes from series-71
2239
            version="3.1.3"/>
2240
    <dependencies>
2241
      <dep package="py"/>
2242
      <dep package="python"/>
2243
    </dependencies>
2244
  </distutils>
2245
2246
  <distutils id="pytest-xdist">
1300 by ccp4
update location of pypi branches
2247
    <branch repo="pypi" module="90/03/1d6a1ab90f6cdfc62a36d93fc341db1384a97a24ed9c5ea0e4004d70c8a3/pytest-xdist-1.18.1.tar.gz"
1284 by Charles Ballard
try to merge in changes from series-71
2248
            version="1.18.1"/>
2249
    <dependencies>
2250
      <dep package="pytest"/>
2251
      <dep package="execnet"/>
2252
    </dependencies>
2253
  </distutils>
2254
2255
  <distutils id="apipkg">
1300 by ccp4
update location of pypi branches
2256
    <branch repo="pypi" module="52/b7/046127821e93d8114338e9431ff896e3cf076e5e510c9ded4cf812af8de5/apipkg-1.2.zip"
1284 by Charles Ballard
try to merge in changes from series-71
2257
            version="1.2" />
2258
  </distutils>
2259
2260
  <distutils id="execnet">
1300 by ccp4
update location of pypi branches
2261
    <branch repo="pypi" module="eb/ee/43729e7dee8772e69b3b01715ab9742790be2eace2d18cf53d219b9c31f8/execnet-1.4.1.tar.gz"
1284 by Charles Ballard
try to merge in changes from series-71
2262
            version="1.4.1" />
2263
    <dependencies/>
2264
    <after>
2265
      <dep package="python"/>
2266
      <dep package="apipkg"/>
2267
    </after>
2268
  </distutils>
2269
1332 by Charles Ballard
move of ccpem to gitlab
2270
<!--  <repository type="svn" name="ccpforge"
2271
              href="https://anonymous@ccpforge.cse.rl.ac.uk/svn/"/> -->
1284 by Charles Ballard
try to merge in changes from series-71
2272
  <cmake id="ccpem">
1332 by Charles Ballard
move of ccpem to gitlab
2273
    <branch repo="gitlab" module="ccpem/ccpem"/>
1284 by Charles Ballard
try to merge in changes from series-71
2274
    <dependencies>
2275
      <dep package="modeller"/>
2276
      <dep package="ccp4-base"/>
2277
      <dep package="libccp4"/>
2278
      <dep package="ccp4-lib-data"/>
2279
      <dep package="mmdb2"/>
2280
      <dep package="clipper"/>
2281
      <dep package="clipper-progs"/>
2282
      <dep package="python"/>
2283
      <dep package="numpy"/>
2284
      <dep package="scipy"/>
2285
      <dep package="pandas"/>
2286
      <dep package="pillow"/>
1332 by Charles Ballard
move of ccpem to gitlab
2287
      <dep package="conkit"/>
1284 by Charles Ballard
try to merge in changes from series-71
2288
      <dep package="pytest"/>
2289
      <dep package="pytest-xdist"/>
2290
      <dep package="biopython"/>
2291
      <dep package="matplotlib"/>
2292
      <dep package="clipper-python"/>
2293
      <dep package="jsrview"/>
2294
      <dep package="molrep"/>
2295
      <dep package="refmac"/>
2296
      <dep package="sfcheck"/>
2297
      <dep package="monomers"/>
2298
      <dep package="ccp4-progs"/>
2299
      <dep package="mrcfile"/>
1314 by ccp4
add patch for hdf5 on mingw
2300
      <dep package="coot"/>
1284 by Charles Ballard
try to merge in changes from series-71
2301
      <dep package="prosmart"/>
2302
      <dep package="xssp"/>
1332 by Charles Ballard
move of ccpem to gitlab
2303
<!--      <dep package="loc-scale"/>-->
2304
<!--      <dep package="mpi4py"/>-->
1284 by Charles Ballard
try to merge in changes from series-71
2305
    </dependencies>
2306
  </cmake>
2307
2308
  <distutils id="mrcfile">
2309
    <branch repo="github" module="ccpem/mrcfile.git"/>
2310
    <dependencies>
2311
      <dep package="numpy"/>
2312
    </dependencies>
2313
  </distutils>
2314
1337 by Charles Ballard
loc-scale stubs, commented out
2315
<!--  <repository type="tarball" name="git-lab" href="https://git.embl.de"/>-->
2316
<!--  <distutils id="loc-scale">-->
2317
<!--    <branch repo="git-lab" module="jakobi/LocScale/raw/master/download/locscale.tgz"-->
2318
<!--            version="0.1"/>-->
2319
<!--    <after>-->
2320
<!--      <dep package="python"/>-->
2321
<!--      <dep package="numpy"/>-->
2322
<!--    </after>-->
2323
<!--  </distutils>-->
2324
2325
2326
<!--  <repository type="git" name="git-lab" href="https://git.embl.de"/>-->
2327
<!--  <distutils id="loc-scale">-->
2328
<!--    <branch repo="git-lab" module="jakobi/LocScale"/>-->
2329
<!--    <dependencies>-->
2330
<!--      <dep package="numpy"/>-->
2331
<!--    </dependencies>-->
2332
<!--  </distutils>-->
2333
1339 by Charles Ballard
correct morda-mp download location
2334
<!--  <repository type="tarball" name="openmpi" -->
2335
<!--          href="https://www.open-mpi.org/software/ompi/v3.0/downloads/"/> -->
2336
<!--    <custom id="openmpi" -->
2337
<!--      configure="./configure \-\-prefix=${prefix}" -->
2338
<!--      build="make" clean="make clean" -->
2339
<!--      install="touch install_docs; make INSTALL_PREFIX=${destdir} install"/> -->
2340
<!--    <pkg-config>openssl.pc</pkg-config> -->
2341
<!--    <branch repo="openmpi" module="openmpi-${version}.tar.gz" -->
2342
<!--            version="3.0.0"> -->
2343
<!--    </branch> -->
2344
<!--  </custom> -->
2345
1335 by Charles Ballard
openmp stub for mpi4py
2346
<!--  <distutils id="mpi4py">
1314 by ccp4
add patch for hdf5 on mingw
2347
    <branch repo="pypi" module="ee/b8/f443e1de0b6495479fc73c5863b7b5272a4ece5122e3589db6cd3bb57eeb/mpi4py-${version}.tar.gz"
2348
            version="2.0.0"/>
2349
    <dependencies>
1335 by Charles Ballard
openmp stub for mpi4py
2350
      <dep package="openmpi"/>
1314 by ccp4
add patch for hdf5 on mingw
2351
      <dep package="numpy"/>
2352
      <dep package="scipy"/>
2353
    </dependencies>
1335 by Charles Ballard
openmp stub for mpi4py
2354
  </distutils> -->
1314 by ccp4
add patch for hdf5 on mingw
2355
1 by Marcin Wojdyr
initial revision of jhbuild config
2356
</moduleset>
6 by Marcin Wojdyr
added pisa
2357
<!-- vim:set ts=2 sw=2 expandtab: -->