/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"
1196 by ronan.keegan at ac
Fix for cock up
10
              href="bzr+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/"/>
71 by Marcin Wojdyr
added cmake to the modules
21
957 by Marcin Wojdyr
updates for ccp4-core -> ccp4-base, ... transition
22
  <custom id="ccp4-base" install_to="* ./">
23
    <branch/>
24
  </custom>
25
1 by Marcin Wojdyr
initial revision of jhbuild config
26
  <autotools id="mmdb">
62 by Marcin Wojdyr
updated ccp4-jhbuild
27
    <branch/>
1 by Marcin Wojdyr
initial revision of jhbuild config
28
  </autotools>
29
673 by Marcin Wojdyr
ccp4.xml: added mmdb2
30
  <autotools id="mmdb2">
31
    <branch/>
32
  </autotools>
33
388 by Marcin Wojdyr
ccp4.xml: add --datadir=${prefix}/lib/data to libccp4
34
  <autotools id="libccp4" autogenargs="--datadir=${prefix}/lib/data">
35
    <branch/>
36
    <dependencies>
957 by Marcin Wojdyr
updates for ccp4-core -> ccp4-base, ... transition
37
      <dep package="ccp4-base"/>
868 by Marcin Wojdyr
libccp4 is linked now with mmdb2
38
      <dep package="mmdb2"/>
388 by Marcin Wojdyr
ccp4.xml: add --datadir=${prefix}/lib/data to libccp4
39
    </dependencies>
40
  </autotools>
41
183 by Marcin Wojdyr
minor updated here and there
42
  <autotools id="ccif" autogenargs="--with-ccp4">
168 by Marcin Wojdyr
a few updates to the moduleset
43
    <branch/>
183 by Marcin Wojdyr
minor updated here and there
44
    <dependencies>
45
      <dep package="libccp4"/>
46
    </dependencies>
492 by Marcin Wojdyr
ccp4.xml: changes in libgnurx
47
    <after>
48
      <dep package="libgnurx"/> <!-- may be needed on Windows only -->
49
    </after>
1 by Marcin Wojdyr
initial revision of jhbuild config
50
  </autotools>
51
46 by Marcin Wojdyr
added gesamt to build script
52
  <autotools id="ssm" autogenargs="--enable-ccp4">
62 by Marcin Wojdyr
updated ccp4-jhbuild
53
    <branch/>
1 by Marcin Wojdyr
initial revision of jhbuild config
54
    <dependencies>
678 by Marcin Wojdyr
ccp4.xml: add mmdb2 as (future) dependency for ssm, pisa, etc
55
      <dep package="mmdb2"/>
1 by Marcin Wojdyr
initial revision of jhbuild config
56
      <dep package="libccp4"/>
57
    </dependencies>
58
  </autotools>
59
691 by Marcin Wojdyr
ccp4.xml: gesamt using now cmake and mmdb2
60
  <cmake id="gesamt" cmakeargs="-DUSE_CCP4=1">
62 by Marcin Wojdyr
updated ccp4-jhbuild
61
    <branch/>
46 by Marcin Wojdyr
added gesamt to build script
62
    <dependencies>
678 by Marcin Wojdyr
ccp4.xml: add mmdb2 as (future) dependency for ssm, pisa, etc
63
      <dep package="mmdb2"/>
46 by Marcin Wojdyr
added gesamt to build script
64
      <dep package="libccp4"/>
1242 by Marcin Wojdyr
gesamt now depends on jsrview
65
      <dep package="jsrview"/>
46 by Marcin Wojdyr
added gesamt to build script
66
    </dependencies>
691 by Marcin Wojdyr
ccp4.xml: gesamt using now cmake and mmdb2
67
  </cmake>
46 by Marcin Wojdyr
added gesamt to build script
68
1 by Marcin Wojdyr
initial revision of jhbuild config
69
  <autotools id="ccp4srs">
62 by Marcin Wojdyr
updated ccp4-jhbuild
70
    <branch/>
1 by Marcin Wojdyr
initial revision of jhbuild config
71
    <dependencies>
678 by Marcin Wojdyr
ccp4.xml: add mmdb2 as (future) dependency for ssm, pisa, etc
72
      <dep package="mmdb2"/>
137 by Marcin Wojdyr
ccp4srs now depends on zlib
73
      <dep package="zlib"/>
232 by Marcin Wojdyr
disable parallel building (make -jN) of FFTW2, it sometimes goes wrong
74
      <dep package="ccp4srs-data"/>
1 by Marcin Wojdyr
initial revision of jhbuild config
75
    </dependencies>
76
  </autotools>
77
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
78
  <custom id="ccp4srs-data"
263 by Marcin Wojdyr
use xia2 from svn (again), avoid copying .bzr/.svn dirs on install
79
          install_to="* share/ccp4srs/">
1042 by Marcin Wojdyr
update ccp4srs-data
80
    <branch repo="ccp4-tarballs" version="20150205"
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
81
            module="ccp4srs-data-${version}.tar.gz"/>
82
  </custom>
83
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
84
  <cmake id="qtlibs">
85
    <branch/>
86
    <dependencies>
87
    </dependencies>
88
  </cmake>
89
297 by Marcin Wojdyr
moduleset: added pseudo-module pisa-no-qt
90
  <!-- special case, building pisa without qtpisa -->
91
  <cmake id="pisa-no-qt" cmakeargs="-DUSE_QT=OFF">
92
    <branch module="pisa"/>
93
    <dependencies>
678 by Marcin Wojdyr
ccp4.xml: add mmdb2 as (future) dependency for ssm, pisa, etc
94
      <dep package="mmdb2"/>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
95
      <dep package="ssm"/>
297 by Marcin Wojdyr
moduleset: added pseudo-module pisa-no-qt
96
      <dep package="libccp4"/>
97
      <dep package="ccp4srs"/>
98
      <dep package="ccp4srs-data"/>
99
    </dependencies>
100
  </cmake>
101
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
102
  <cmake id="pisa">
62 by Marcin Wojdyr
updated ccp4-jhbuild
103
    <branch/>
6 by Marcin Wojdyr
added pisa
104
    <dependencies>
678 by Marcin Wojdyr
ccp4.xml: add mmdb2 as (future) dependency for ssm, pisa, etc
105
      <dep package="mmdb2"/>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
106
      <dep package="ssm"/>
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
107
      <dep package="libccp4"/>
6 by Marcin Wojdyr
added pisa
108
      <dep package="ccp4srs"/>
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
109
      <dep package="ccp4srs-data"/>
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
110
      <dep package="qtlibs"/>
6 by Marcin Wojdyr
added pisa
111
    </dependencies>
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
112
  </cmake>
6 by Marcin Wojdyr
added pisa
113
114
  <cmake id="refmac">
290 by Marcin Wojdyr
refmac: change directory name to refmac5.8 to avoid conflicts on update
115
    <branch branch="5.8" checkoutdir="refmac5.8"/>
7 by Marcin Wojdyr
added refmac
116
    <dependencies>
117
      <dep package="libccp4"/>
118
      <dep package="lapack"/>
886 by Marcin Wojdyr
ccp4.xml: refmac now requires FFTW2
119
      <dep package="fftw2"/>
7 by Marcin Wojdyr
added refmac
120
    </dependencies>
6 by Marcin Wojdyr
added pisa
121
  </cmake>
122
190 by Marcin Wojdyr
moduleset changes: new LAPACK, refmac_dictionary is now in bazaar
123
  <custom id="monomers"
263 by Marcin Wojdyr
use xia2 from svn (again), avoid copying .bzr/.svn dirs on install
124
      install_to="* lib/data/monomers/">
190 by Marcin Wojdyr
moduleset changes: new LAPACK, refmac_dictionary is now in bazaar
125
    <branch/>
126
    <!--
183 by Marcin Wojdyr
minor updated here and there
127
    <branch repo="refmac_experimental" version="5.38"
150 by Marcin Wojdyr
misc changes
128
            module="refmac_dictionary_v${version}.tar.gz"
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
129
            checkoutdir="refmac_dictionary_v${version}"/>
190 by Marcin Wojdyr
moduleset changes: new LAPACK, refmac_dictionary is now in bazaar
130
    -->
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
131
  </custom>
85 by Marcin Wojdyr
added refmac_dictionary to modules
132
15 by Marcin Wojdyr
added ccp4 from CVS (with cmake) to ccp4.modules
133
  <cmake id="ccp4-progs">
219 by Marcin Wojdyr
updated moduleset to add new bzr modules
134
    <branch/>
15 by Marcin Wojdyr
added ccp4 from CVS (with cmake) to ccp4.modules
135
    <dependencies>
136
      <dep package="libccp4"/>
186 by Marcin Wojdyr
ccp4-progs depends on ccif
137
      <dep package="ccif"/>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
138
      <dep package="mmdb2"/>
15 by Marcin Wojdyr
added ccp4 from CVS (with cmake) to ccp4.modules
139
    </dependencies>
140
  </cmake>
141
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
142
  <custom id="examples"
263 by Marcin Wojdyr
use xia2 from svn (again), avoid copying .bzr/.svn dirs on install
143
          install_to="* examples/">
314 by Marcin Wojdyr
use bzr checkout --light for mrbump, examples and ccp4-core
144
    <branch light="yes"/> <!-- whole repo is big, 280MB -->
175 by Marcin Wojdyr
added 'custom' module type to jhbuild
145
  </custom>
147 by Marcin Wojdyr
misc updates
146
177 by Marcin Wojdyr
updated moduleset
147
  <custom id="documentation"
922 by Marcin Wojdyr
use documentation/installer.sh script for installing documentation
148
          install="./installer.sh ${dest}">
177 by Marcin Wojdyr
updated moduleset
149
    <branch/>
150
  </custom>
151
957 by Marcin Wojdyr
updates for ccp4-core -> ccp4-base, ... transition
152
  <custom id="ccp4-lib-data" install_to="* lib/data/">
153
    <branch repo="files" module="ccp4-lib-data-6.5.0.tar.gz"
154
            size="15269420" version="6.5.0"/>
155
  </custom>
156
597 by Marcin Wojdyr
ccp4.xml: added test-sys (download-only)
157
  <custom id="test-sys">
158
    <branch/>
159
  </custom>
160
29 by Marcin Wojdyr
added ccp4i to build script
161
  <cmake id="ccp4i">
168 by Marcin Wojdyr
a few updates to the moduleset
162
    <branch/>
163
  </cmake>
164
263 by Marcin Wojdyr
use xia2 from svn (again), avoid copying .bzr/.svn dirs on install
165
  <custom id="imosflm" install_to="* share/ccp4i/imosflm/">
219 by Marcin Wojdyr
updated moduleset to add new bzr modules
166
    <branch/>
167
  </custom>
168
723 by Marcin Wojdyr
ccp4.xml: added hklfile
169
  <cmake id="hklfile">
170
    <branch/>
907 by Marcin Wojdyr
ccp4.xml: specify deps for hklfile
171
    <dependencies>
172
      <dep package="libccp4"/>
173
      <dep package="clipper"/>
174
    </dependencies>
723 by Marcin Wojdyr
ccp4.xml: added hklfile
175
  </cmake>
176
168 by Marcin Wojdyr
a few updates to the moduleset
177
  <cmake id="viewhkl">
178
    <branch/>
185 by Marcin Wojdyr
moduleset: add viewhkl dependencies
179
    <dependencies>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
180
      <dep package="mmdb2"/>
185 by Marcin Wojdyr
moduleset: add viewhkl dependencies
181
      <dep package="libccp4"/>
182
      <dep package="clipper"/>
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
183
      <dep package="qtlibs"/>
723 by Marcin Wojdyr
ccp4.xml: added hklfile
184
      <dep package="hklfile"/>
185 by Marcin Wojdyr
moduleset: add viewhkl dependencies
185
    </dependencies>
168 by Marcin Wojdyr
a few updates to the moduleset
186
  </cmake>
187
220 by Marcin Wojdyr
added qtrview
188
  <cmake id="qtrview">
189
    <branch/>
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
190
    <dependencies>
191
      <dep package="qtlibs"/>
192
    </dependencies>
220 by Marcin Wojdyr
added qtrview
193
  </cmake>
194
960 by Andrey Lebedev
jsrview build corrected
195
  <cmake id="jsrview">
586 by Marcin Wojdyr
ccp4.xml: added download-only jsrview module
196
    <branch/>
1282 by Andrey Lebedev
added morda-mp
197
<!--
586 by Marcin Wojdyr
ccp4.xml: added download-only jsrview module
198
    <dependencies>
199
      <dep package="qtlibs"/>
200
    </dependencies>
1282 by Andrey Lebedev
added morda-mp
201
-->
960 by Andrey Lebedev
jsrview build corrected
202
  </cmake>
586 by Marcin Wojdyr
ccp4.xml: added download-only jsrview module
203
168 by Marcin Wojdyr
a few updates to the moduleset
204
  <cmake id="setup">
205
    <branch/>
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
206
    <dependencies>
207
      <dep package="qtlibs"/>
208
    </dependencies>
168 by Marcin Wojdyr
a few updates to the moduleset
209
  </cmake>
210
1181 by ronan.keegan at ac
updated mrbump installer and update to hmmer location
211
<!--
275 by Marcin Wojdyr
added dssp (for now) to nonportable section, copy mrbump files instead of
212
  <custom id="mrbump"
213
          install_to="bin/* bin/, data share/mrbump/, include share/mrbump/">
314 by Marcin Wojdyr
use bzr checkout --light for mrbump, examples and ccp4-core
214
    <branch light="yes"/>
803 by Marcin Wojdyr
ccp4.xml: added soft dependencies to mrbump and ample
215
    <suggests>
880 by Marcin Wojdyr
add HMMER
216
      <dep package="hmmer"/>
803 by Marcin Wojdyr
ccp4.xml: added soft dependencies to mrbump and ample
217
      <dep package="mafft"/>
218
      <dep package="clustalw2"/>
219
    </suggests>
275 by Marcin Wojdyr
added dssp (for now) to nonportable section, copy mrbump files instead of
220
  </custom>
1181 by ronan.keegan at ac
updated mrbump installer and update to hmmer location
221
-->
222
223
  <cmake id="mrbump">
224
    <branch/>
225
    <dependencies>
226
      <dep package="hmmer"/>
227
      <dep package="mafft"/>
228
      <dep package="clustalw2"/>
229
    </dependencies>
230
  </cmake>
146 by Marcin Wojdyr
updated moduleset
231
1277 by Tom Burnley
update to include modeller dep for ccpem
232
  <custom id="modeller" install_to="* lib/modeller/">
233
    <branch repo="files" module="https://salilab.org/modeller/9.19/modeller-9.19.tar.gz"
234
            version="9.19"/>
235
  </custom>
236
247 by Marcin Wojdyr
ccp4.xml: added dssp to to modulset (although not to "all" meta-module yet)
237
  <cmake id="dssp">
238
    <branch/>
679 by Marcin Wojdyr
ccp4.xml & conf.py: build boost with python and cctbx with external boost
239
    <dependencies>
372 by Marcin Wojdyr
ccp4.xml: add boost
240
      <dep package="boost"/>
679 by Marcin Wojdyr
ccp4.xml & conf.py: build boost with python and cctbx with external boost
241
    </dependencies>
247 by Marcin Wojdyr
ccp4.xml: added dssp to to modulset (although not to "all" meta-module yet)
242
  </cmake>
243
1113 by Marcin Wojdyr
added xssp
244
  <cmake id="xssp">
245
    <branch repo="github-zip"
246
        module="cmbi/xssp/releases/download/${version}/xssp-${version}.tar.gz"
247
        version="2.2.7" size="236575">
248
      <patch file="xssp.patch" strip="0" />
249
    </branch>
250
    <dependencies>
251
      <dep package="boost"/>
252
    </dependencies>
253
  </cmake>
254
309 by Marcin Wojdyr
ccp4.xml: added tgutils
255
  <cmake id="tgutils">
256
    <branch/>
377 by Marcin Wojdyr
ccp4.xml: add missing dependency
257
    <dependencies>
258
      <dep package="clipper"/>
259
    </dependencies>
309 by Marcin Wojdyr
ccp4.xml: added tgutils
260
  </cmake>
261
284 by Marcin Wojdyr
moduleset: added dimple to default set of packages
262
  <cmake id="dimple">
1202 by Marcin Wojdyr
on Eugene's request, take dimple from bazaar not from git
263
    <!-- directly from git repo:
1178 by Marcin Wojdyr
take dimple from github.com/ccp4/dimple
264
    <branch repo="github" module="ccp4/dimple.git"/>
1202 by Marcin Wojdyr
on Eugene's request, take dimple from bazaar not from git
265
    or from ccp4 bzr repo: -->
266
    <branch/>
286 by Marcin Wojdyr
moduleset: dimple depends on clipper
267
    <dependencies>
268
      <dep package="clipper"/>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
269
      <dep package="mmdb2"/>
286 by Marcin Wojdyr
moduleset: dimple depends on clipper
270
    </dependencies>
284 by Marcin Wojdyr
moduleset: added dimple to default set of packages
271
  </cmake>
236 by Marcin Wojdyr
moduleset: added ample and dimple
272
1285 by ronan.keegan at ac
Take ample from head of trunk
273
<!--    <branch repo="github-zip"
1284 by ronan.keegan at ac
update ccp4.xml for ample/simbad
274
            version="1.2.1"
275
            module="rigdenlab/ample/archive/${version}.zip"
276
            checkoutdir="ample-${version}">
1285 by ronan.keegan at ac
Take ample from head of trunk
277
    </branch>-->
278
279
  <cmake id="ample">
280
    <branch repo="github" module="rigdenlab/ample.git"/>
1195 by ronan.keegan at ac
AMPLE now cmake and module in python
281
    <dependencies>
1284 by ronan.keegan at ac
update ccp4.xml for ample/simbad
282
      <dep package="numpy"/>
283
      <dep package="conkit"/>
284
      <dep package="matplotlib"/>
285
      <dep package="biopython"/>
286
      <dep package="pandas"/>
1195 by ronan.keegan at ac
AMPLE now cmake and module in python
287
      <dep package="theseus"/>
288
      <dep package="spicker"/>
1284 by ronan.keegan at ac
update ccp4.xml for ample/simbad
289
      <dep package="mrbump"/>
1195 by ronan.keegan at ac
AMPLE now cmake and module in python
290
    </dependencies>
291
  </cmake>
236 by Marcin Wojdyr
moduleset: added ample and dimple
292
1082 by Marcin Wojdyr
update SWIG to 3.0.6
293
  <autotools id="swig" autogenargs="--bindir=${prefix}/devbin --without-pcre --disable-ccache --without-ocaml">
592 by Charles Ballard
add swig for mg build, needed on osx unless have already installed
294
    <branch repo="sf" module="swig/swig-${version}.tar.gz"
1100 by Marcin Wojdyr
update swig 3.0.6 to 3.0.7
295
            version="3.0.7" size="5923046"/>
592 by Charles Ballard
add swig for mg build, needed on osx unless have already installed
296
  </autotools>
297
542 by Marcin Wojdyr
update ccp4mg in ccp4.xml (but it's not working yet)
298
  <cmake id="ccp4mg">
748 by Marcin Wojdyr
ccp4.xml: switch ccp4mg from branch ccp4-jhbuild-distutils to branch ccp4
299
    <branch branch="ccp4"/>
546 by Marcin Wojdyr
some dependencies for ccp4mg
300
    <dependencies>
301
      <dep package="clipper"/>
789 by Marcin Wojdyr
ccp4.xml: add hklfile to MG dependencies
302
      <dep package="hklfile"/>
546 by Marcin Wojdyr
some dependencies for ccp4mg
303
      <dep package="ssm"/>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
304
      <dep package="mmdb2"/>
546 by Marcin Wojdyr
some dependencies for ccp4mg
305
      <dep package="libccp4"/>
1058 by Marcin Wojdyr
ccp4.xml: mg depends on ccp4srs
306
      <dep package="ccp4srs"/>
593 by Charles Ballard
pyqt4 as explicit dependency for ccp4mg
307
      <dep package="pyqt4"/>
1023 by Marcin Wojdyr
modified dependecies: added ccp4mg to "default", pixie and matplotlib to ccp4mg,
308
      <dep package="rdkit"/>
625 by Marcin Wojdyr
ccp4.xml: add suds and lxml as dependencies of MG
309
      <!-- below are runtime dependencies, kind of optional -->
310
      <dep package="suds"/>
311
      <dep package="lxml"/>
1023 by Marcin Wojdyr
modified dependecies: added ccp4mg to "default", pixie and matplotlib to ccp4mg,
312
      <dep package="matplotlib"/>
313
      <dep package="pixie"/>
546 by Marcin Wojdyr
some dependencies for ccp4mg
314
    </dependencies>
542 by Marcin Wojdyr
update ccp4mg in ccp4.xml (but it's not working yet)
315
  </cmake>
242 by Marcin Wojdyr
updated README and ccp4.xml
316
903 by Marcin Wojdyr
ccp4.xml: use cmake for i2
317
  <cmake id="ccp4i2">
867 by Marcin Wojdyr
ccp4.xml & misc/watch-repos.py: add ccp4i2 repo
318
    <branch/>
903 by Marcin Wojdyr
ccp4.xml: use cmake for i2
319
  </cmake>
867 by Marcin Wojdyr
ccp4.xml & misc/watch-repos.py: add ccp4i2 repo
320
188 by Marcin Wojdyr
jligand is now in bazaar
321
  <custom id="jligand"
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
322
          build="make" clean="make clean"
277 by Marcin Wojdyr
added hklview and a few other modules
323
          install_to="JLigand.jar bin/, jligand bin/">
188 by Marcin Wojdyr
jligand is now in bazaar
324
    <branch/>
177 by Marcin Wojdyr
updated moduleset
325
  </custom>
99 by Marcin Wojdyr
minor changes in moduleset and in docs
326
168 by Marcin Wojdyr
a few updates to the moduleset
327
  <cmake id="molrep">
328
    <branch/>
329
    <dependencies>
330
      <dep package="libccp4"/>
331
    </dependencies>
332
  </cmake>
333
177 by Marcin Wojdyr
updated moduleset
334
  <cmake id="sfcheck">
335
    <branch/>
336
    <dependencies>
337
      <dep package="libccp4"/>
338
    </dependencies>
339
  </cmake>
340
206 by Marcin Wojdyr
moduleset: build procheck from bazaar
341
  <cmake id="procheck">
342
    <branch/>
343
    <dependencies>
344
      <dep package="libccp4"/>
345
    </dependencies>
346
  </cmake>
347
219 by Marcin Wojdyr
updated moduleset to add new bzr modules
348
  <cmake id="scala">
349
    <branch/>
350
    <dependencies>
351
      <dep package="libccp4"/>
352
      <dep package="lapack"/>
353
    </dependencies>
354
  </cmake>
355
356
  <cmake id="dm21">
357
    <branch/>
358
    <dependencies>
359
      <dep package="libccp4"/>
360
      <dep package="ccif"/>
361
    </dependencies>
362
  </cmake>
363
364
  <cmake id="ccp4-deprecated">
365
    <branch/>
366
    <dependencies>
367
      <dep package="libccp4"/>
368
      <dep package="ccif"/>
369
      <dep package="lapack"/>
370
    </dependencies>
371
  </cmake>
372
890 by Marcin Wojdyr
ccp4.xml: use cmake for edstats, to make things easier
373
  <cmake id="edstats">
279 by Marcin Wojdyr
moduleset: added edstats
374
    <branch/>
283 by Marcin Wojdyr
moduleset: edstats depends on libccp4
375
    <dependencies>
376
      <dep package="libccp4"/>
377
    </dependencies>
890 by Marcin Wojdyr
ccp4.xml: use cmake for edstats, to make things easier
378
  </cmake>
279 by Marcin Wojdyr
moduleset: added edstats
379
537 by Marcin Wojdyr
ccp4.xml: another fix in the same place
380
  <autotools id="mosflm" skip-autogen="never"
381
             autogenargs="--with-ccp4-prefix=${prefix}"
536 by Marcin Wojdyr
fix ccp4.xml
382
             supports-non-srcdir-builds="no" makeargs="-j1 clean all">
535 by Marcin Wojdyr
ccp4.xml: use mosflm from bzr
383
  <branch/>
399 by Marcin Wojdyr
added mosflm
384
    <dependencies>
385
      <dep package="libccp4"/>
386
      <dep package="xdl-view"/>
387
    </dependencies>
388
  </autotools>
389
394 by Marcin Wojdyr
add note about Xt
390
  <!-- requires libxt-dev/libXt-devel -->
277 by Marcin Wojdyr
added hklview and a few other modules
391
  <autotools id="xdl-view" autogen-sh="src/configure">
392
    <branch/>
393
  </autotools>
394
395
  <cmake id="hklview">
396
    <branch/>
397
    <dependencies>
398
      <dep package="libccp4"/>
399
      <dep package="xdl-view"/>
400
    </dependencies>
401
  </cmake>
402
403
  <autotools id="jwc-c">
404
    <branch/>
405
    <dependencies>
406
      <dep package="libccp4"/>
407
    </dependencies>
408
  </autotools>
409
410
  <autotools id="jwc-f">
411
    <dependencies>
412
      <dep package="jwc-c"/>
413
      <dep package="libccp4"/>
414
    </dependencies>
415
    <branch/>
416
  </autotools>
417
1038 by Marcin Wojdyr
build rotgen using cmake
418
  <cmake id="rotgen">
532 by Marcin Wojdyr
ccp4.xml: use rotgen from bzr
419
    <branch/>
398 by Marcin Wojdyr
added rotgen
420
    <dependencies>
421
      <dep package="jwc-f"/>
422
      <dep package="xdl-view"/>
423
    </dependencies>
1038 by Marcin Wojdyr
build rotgen using cmake
424
  </cmake>
398 by Marcin Wojdyr
added rotgen
425
970 by Marcin Wojdyr
ccp4.xml: install README.USAGE from balbes-pipeline
426
  <custom id="balbes-pipeline" install_to="README.USAGE BALBES/, Package/* BALBES/">
969 by Marcin Wojdyr
ccp4.xml: added balbesdb and metamodule balbes
427
    <branch/>
428
  </custom>
429
430
  <custom id="balbesdb" install_to="Package/* BALBES/">
277 by Marcin Wojdyr
added hklview and a few other modules
431
    <branch/>
432
  </custom>
433
434
  <autotools id="dl-laue">
435
    <branch branch="laue/trunk"/>
436
  </autotools>
224 by Marcin Wojdyr
added ccp4-progs to moduleset
437
416 by Marcin Wojdyr
ccp4.xml: install ccp4dispatchers/releaseme/* to libexec/
438
  <custom id="ccp4dispatchers"
439
          install_to="releaseme/* libexec/">
358 by Marcin Wojdyr
small fixes
440
    <branch/>
441
  </custom>
442
365 by Marcin Wojdyr
minor tweaks
443
  <custom id="devtools"> <!-- only for use in bundling script -->
444
    <branch/>
445
  </custom>
446
959 by Marcin Wojdyr
ccp4.xml: coot --without-enhanced-... doesn't work as expected, removed
447
  <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)
448
    <branch branch="old-trunk" light="yes"/>
219 by Marcin Wojdyr
updated moduleset to add new bzr modules
449
  </cmake>
450
136 by Marcin Wojdyr
updates
451
  <autotools id="clipper" autogen-sh="configure"
528 by Marcin Wojdyr
ccp4.xml: no need to --enable-fortran in clipper
452
      autogenargs="--enable-ccp4 --enable-mmdb --enable-cif --enable-minimol">
136 by Marcin Wojdyr
updates
453
    <branch/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
454
    <dependencies>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
455
      <dep package="mmdb2"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
456
      <dep package="libccp4"/>
98 by Marcin Wojdyr
updated moduleset
457
      <dep package="fftw2"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
458
    </dependencies>
459
  </autotools>
460
1065 by Marcin Wojdyr
add clipper-python and ccp4srs-python to the build
461
  <cmake id="clipper-python">
462
    <branch branch="trunk"/>
463
    <dependencies>
1296 by Tom Burnley
add lxml dep for clipper python
464
      <dep package="lxml"/>
1065 by Marcin Wojdyr
add clipper-python and ccp4srs-python to the build
465
      <dep package="libccp4"/>
466
      <dep package="clipper"/>
1194 by Marcin Wojdyr
clipper-python depends now on numpy
467
      <dep package="numpy"/>
1065 by Marcin Wojdyr
add clipper-python and ccp4srs-python to the build
468
    </dependencies>
469
  </cmake>
470
471
  <cmake id="ccp4srs-python">
472
    <branch branch="trunk"/>
473
    <dependencies>
474
      <dep package="ccp4srs"/>
475
    </dependencies>
476
  </cmake>
477
211 by Marcin Wojdyr
updated moduleset
478
  <!-- cctbx w/ phaser (phaser can be build only as cctbx subdirectory) -->
368 by Marcin Wojdyr
ccp4.xml: use custom module type for cctbx
479
  <custom id="cctbx-phaser"
480
          configure="sh ${srcdir}/autogen.sh ${prefix} ${libdir}"
481
          build="${}" install="${}" clean="${}"
482
          supports-non-srcdir-builds="yes">
1247 by Charles Ballard
use cctbx version bundled as latest on our site
483
    <branch repo="files" version="latest"
1250 by Charles Ballard
set checkoutdir for cctbx-phaser, back ported from release branches
484
            module="cctbx-phaser-dials-${version}.tar.gz"
485
            checkoutdir="cctbx-phaser" >
63 by Marcin Wojdyr
updated ccp4-jhbuild
486
      <patch file="cctbx-autogen.patch" strip="0" />
251 by Marcin Wojdyr
updated cctbx/phaser to current nightly built version
487
      <patch file="cctbx-no-unroll.patch" strip="0" />
255 by Marcin Wojdyr
added patch to cctbx to suppport LDFLAGS env var.
488
      <patch file="cctbx-ldflags.patch" strip="0" />
448 by Marcin Wojdyr
added patch for compilation of cctbx/annlib with MinGW
489
      <patch file="cctbx-ann-mingw.patch" strip="0" />
509 by Charles Ballard
add patches for intel compilers on mac to cctbx
490
      <patch file="cctbx-icc.patch" strip="0" />
679 by Marcin Wojdyr
ccp4.xml & conf.py: build boost with python and cctbx with external boost
491
      <patch file="cctbx-system-boost.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"/>
679 by Marcin Wojdyr
ccp4.xml & conf.py: build boost with python and cctbx with external boost
496
    </dependencies>
368 by Marcin Wojdyr
ccp4.xml: use custom module type for cctbx
497
  </custom>
63 by Marcin Wojdyr
updated ccp4-jhbuild
498
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
499
  <repository type="tarball" name="pre_ftp"
500
              href="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
501
  <cmake id="pointless">
360 by Marcin Wojdyr
ccp4.xml: switch pointless to light checkout (normal checkout can be long)
502
    <branch light="yes"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
503
    <dependencies>
504
      <dep package="clipper"/>
505
      <dep package="libccp4"/>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
506
      <dep package="cctbx-phaser"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
507
    </dependencies>
508
  </cmake>
509
510
  <cmake id="aimless">
303 by Marcin Wojdyr
moduleset: take pointless and aimless from bazaar
511
    <branch/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
512
    <dependencies>
513
      <dep package="clipper"/>
514
      <dep package="libccp4"/>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
515
      <dep package="cctbx-phaser"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
516
    </dependencies>
517
  </cmake>
518
670 by Charles Ballard
trunk gets feckless build
519
  <cmake id="feckless">
672 by Marcin Wojdyr
ccp4.xml: fix 'feckless' entry
520
    <branch/>
670 by Charles Ballard
trunk gets feckless build
521
    <dependencies>
522
      <dep package="clipper"/>
523
      <dep package="libccp4"/>
524
      <dep package="cctbx-phaser"/>
525
    </dependencies>
526
  </cmake>
527
1040 by Marcin Wojdyr
ccp4.xml: use cmake for clipper-progs
528
  <cmake id="clipper-progs">
62 by Marcin Wojdyr
updated ccp4-jhbuild
529
    <branch/>
56 by Marcin Wojdyr
a few small updates
530
    <dependencies>
531
      <dep package="clipper"/>
532
      <dep package="libccp4"/>
533
    </dependencies>
1040 by Marcin Wojdyr
ccp4.xml: use cmake for clipper-progs
534
  </cmake>
56 by Marcin Wojdyr
a few small updates
535
192 by Marcin Wojdyr
cprodrg is now in bzr, CVS no longer needed
536
  <autotools id="cprodrg">
537
    <branch/>
42 by Marcin Wojdyr
added cmake script for aimless, fixed autogen.sh for cctbx
538
    <dependencies>
69 by Marcin Wojdyr
added some system packages to the build (like zlib)
539
      <dep package="zlib"/>
42 by Marcin Wojdyr
added cmake script for aimless, fixed autogen.sh for cctbx
540
      <dep package="libccp4"/>
541
    </dependencies>
542
  </autotools>
543
794 by Marcin Wojdyr
ccp4.xml: build prosmart using cmake
544
  <cmake id="prosmart">
79 by Marcin Wojdyr
ccp4.xml: added prosmart and updated ccp4-progs
545
    <branch/>
1275 by Tom Burnley
add mmdb2 as dep. for prosmart
546
    <dependencies>
547
      <dep package="mmdb2"/>
548
    </dependencies>
794 by Marcin Wojdyr
ccp4.xml: build prosmart using cmake
549
  </cmake>
79 by Marcin Wojdyr
ccp4.xml: added prosmart and updated ccp4-progs
550
885 by Marcin Wojdyr
ccp4.xml: added restraint-valid, whatever it is, just for download
551
  <custom id="restraint-valid">
552
    <branch/>
553
  </custom>
554
792 by Marcin Wojdyr
ccp4.xml: added acedrg
555
  <cmake id="acedrg">
795 by Marcin Wojdyr
ccp4.xml: acedrg - use light checkout
556
    <branch light="yes"/>
792 by Marcin Wojdyr
ccp4.xml: added acedrg
557
    <dependencies>
1073 by Charles Ballard
ccp4i2 dependencies biopython and jsrview are reinstated.
558
       <dep package="rdkit"/>
792 by Marcin Wojdyr
ccp4.xml: added acedrg
559
    </dependencies>
560
  </cmake>
561
906 by Marcin Wojdyr
ccp4.xml: add libg
562
  <cmake id="libg">
563
    <branch/>
564
  </cmake>
565
858 by Marcin Wojdyr
ccp4.xml: add privateer
566
  <cmake id="privateer">
567
    <branch/>
568
    <dependencies>
569
      <dep package="clipper"/>
1129 by Marcin Wojdyr
ccp4.xml: privateer now depends on ccp4srs
570
      <dep package="ccp4srs"/>
858 by Marcin Wojdyr
ccp4.xml: add privateer
571
    </dependencies>
572
  </cmake>
573
47 by Marcin Wojdyr
updated modules list (not tested)
574
  <autotools id="rapper">
628 by Marcin Wojdyr
change rapper tarball, added fix for building with static libxml2
575
    <branch repo="files" module="rapper_ccp4-1.0a.tar.bz2"
576
            size="11337826" version="1.0a"/>
132 by Marcin Wojdyr
updated moduleset
577
    <dependencies>
578
      <dep package="libxml2"/>
579
      <dep package="gc"/>
580
    </dependencies>
47 by Marcin Wojdyr
updated modules list (not tested)
581
  </autotools>
582
215 by Marcin Wojdyr
misc. changes in conf.py and ccp4.xml
583
  <autotools id="diff-image">
172 by Marcin Wojdyr
updated moduleset
584
    <branch/>
115 by Marcin Wojdyr
moduleset: updated diff-image options
585
    <dependencies>
586
      <dep package="libjpeg"/>
122 by Marcin Wojdyr
added ccp4mapwish module
587
    </dependencies>
704 by Marcin Wojdyr
build ccp4mapwish and diff-image after tcltk84
588
    <after>
589
      <dep package="tcltk84"/>
590
    </after>
122 by Marcin Wojdyr
added ccp4mapwish module
591
  </autotools>
592
593
  <autotools id="ccp4mapwish">
594
    <branch/>
595
    <dependencies>
596
      <dep package="libccp4"/>
115 by Marcin Wojdyr
moduleset: updated diff-image options
597
    </dependencies>
704 by Marcin Wojdyr
build ccp4mapwish and diff-image after tcltk84
598
    <after>
599
      <!-- it requires Tcl, but on Windows Tcl must be installed manually -->
600
      <dep package="tcltk84"/>
601
    </after>
88 by Marcin Wojdyr
update c-j
602
  </autotools>
603
1172 by Marcin Wojdyr
crank: use only branch 2.0
604
  <cmake id="crank2" cmakeargs="-DCMAKE_BUILD_TYPE=None">
1186 by Marcin Wojdyr
crank trunk is now 2.0
605
    <branch module="crank"/>
686 by Marcin Wojdyr
ccp4.xml: added crank2
606
    <dependencies>
1172 by Marcin Wojdyr
crank: use only branch 2.0
607
      <dep package="libccp4"/>
608
      <dep package="clipper"/>
609
      <dep package="lapack"/>
1027 by Marcin Wojdyr
ccp4.xml: exclude biopython and jsrview from default
610
      <!--<dep package="jsrview"/>-->
686 by Marcin Wojdyr
ccp4.xml: added crank2
611
    </dependencies>
612
  </cmake>
613
627 by Marcin Wojdyr
ccp4.xml: add blend
614
  <cmake id="blend">
615
    <branch/>
616
    <dependencies>
617
      <dep package="clipper"/>
618
      <dep package="cctbx-phaser"/>
619
    </dependencies>
620
  </cmake>
621
527 by Marcin Wojdyr
add chooch, but don't build it
622
  <cmake id="chooch">
623
    <branch/>
624
    <dependencies>
625
      <dep package="gsl"/>
588 by Marcin Wojdyr
ccp4.xml: added plplot
626
      <dep package="plplot"/>
527 by Marcin Wojdyr
add chooch, but don't build it
627
    </dependencies>
628
  </cmake>
629
647 by ronan.keegan at ac
added spicker build
630
  <cmake id="spicker">
631
    <branch/>
632
  </cmake>
633
742 by ronan.keegan at ac
Added prelyscar to build
634
  <cmake id="prelyscar">
635
    <branch/>
636
  </cmake>
637
1112 by Marcin Wojdyr
new theseus CMakeLists.txt
638
  <repository type="tarball" name="theseus3d"
639
              href="http://www.theseus3d.org/src/"/>
652 by ronan.keegan at ac
Added theseus 2.0.6 to the build
640
  <cmake id="theseus">
1112 by Marcin Wojdyr
new theseus CMakeLists.txt
641
    <branch repo="theseus3d" module="theseus_${version}.tar.gz" version="3.3.0"
642
            size="22548124" checkoutdir="theseus_${version}">
643
      <patch file="theseus.patch" strip="0" />
644
    </branch>
652 by ronan.keegan at ac
Added theseus 2.0.6 to the build
645
    <dependencies>
646
      <dep package="gsl"/>
647
    </dependencies>
648
  </cmake>
649
1293 by Tom Burnley
revert ccpem deps for standard qt4 build
650
  <repository type="tarball" name="openmpi"
651
              href="https://www.open-mpi.org/software/ompi/v3.0/downloads/"/>
652
  <custom id="openmpi"
653
          configure="./configure --prefix=${prefix}"
654
          build="make" clean="make clean"
655
          install="touch install_docs; make INSTALL_PREFIX=${destdir} install">
656
    <pkg-config>openssl.pc</pkg-config>
657
    <branch repo="openmpi" module="openmpi-${version}.tar.gz"
658
            version="3.0.0">
659
    </branch>
660
  </custom>
661
539 by Marcin Wojdyr
ccp4.xml: added clustalw2, preparing mafft
662
  <!-- Unix-only (relies on shell-scripting inside system() call) -->
663
  <!-- <repository type="tarball" name="pdb-extract"
664
              href="http://sw-tools.pdb.org/apps/PDB_EXTRACT/"/> -->
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
665
  <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
666
                           install_to="bin/* bin/">
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
667
    <!-- <branch module="pdb-extract-v3.11-prod-src.tar.gz" repo="pdb-extract"
539 by Marcin Wojdyr
ccp4.xml: added clustalw2, preparing mafft
668
               version="3.11"/> - original tarball doesn't compile of-of-box
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
669
    -->
670
    <branch/>
671
  </custom>
101 by Marcin Wojdyr
updated ccp4-jhbuild
672
880 by Marcin Wojdyr
add HMMER
673
  <repository type="tarball" name="hmmer"
1181 by ronan.keegan at ac
updated mrbump installer and update to hmmer location
674
              href="http://eddylab.org/software/"/>
880 by Marcin Wojdyr
add HMMER
675
  <autotools id="hmmer" autogenargs="--bindir=${prefix}/libexec --enable-sse">
676
    <branch repo="hmmer" module="hmmer3/3.1b1/hmmer-3.1b1.tar.gz"
677
            version="3.1b1" size="5778584"/>
678
  </autotools>
679
539 by Marcin Wojdyr
ccp4.xml: added clustalw2, preparing mafft
680
  <repository type="tarball" name="clustal"
681
              href="http://www.clustal.org/download/current/"/>
682
  <autotools id="clustalw2" autogenargs="--bindir=${prefix}/libexec">
683
    <branch repo="clustal" module="clustalw-2.1.tar.gz"
544 by Marcin Wojdyr
added clustalw2 patch for MinGW, finishing mafft setup
684
            version="2.1" size="350761">
685
      <patch file="clustalw2-time.patch" strip="0" />
662 by Charles Ballard
need string header for clang-5
686
      <patch file="clustalw2-string.patch" strip="0" />
544 by Marcin Wojdyr
added clustalw2 patch for MinGW, finishing mafft setup
687
    </branch>
539 by Marcin Wojdyr
ccp4.xml: added clustalw2, preparing mafft
688
  </autotools>
689
690
  <repository type="tarball" name="mafft"
691
              href="http://mafft.cbrc.jp/alignment/software/"/>
1103 by Marcin Wojdyr
update mafft
692
  <!-- "make -e" overrides CC and CFLAGS in Makefile 
693
       (we could do "sed -i 's/^C/#C/' core/Makefile" instead).
694
       sed hack is needed because BINDIR is the same as  LIBDIR
544 by Marcin Wojdyr
added clustalw2 patch for MinGW, finishing mafft setup
695
  -->
696
  <custom id="mafft"
822 by Marcin Wojdyr
updated mafft
697
      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
698
      build="${} -e -C core -j1 clean all"
1103 by Marcin Wojdyr
update mafft
699
      install="make -C core install DESTDIR=${destdir} PREFIX=${prefix} LIBDIR=${prefix}/libexec BINDIR=${prefix}/libexec"
544 by Marcin Wojdyr
added clustalw2 patch for MinGW, finishing mafft setup
700
      clean="make -C core clean">
896 by Marcin Wojdyr
ccp4.xml: update mafft
701
    <branch repo="mafft" module="mafft-${version}-without-extensions-src.tgz"
702
            checkoutdir="mafft-${version}-without-extensions"
1103 by Marcin Wojdyr
update mafft
703
            version="7.245" size="397503"/>
539 by Marcin Wojdyr
ccp4.xml: added clustalw2, preparing mafft
704
  </custom>
705
320 by Marcin Wojdyr
more coot dependencies
706
<!--
707
install intltool libfontconfig1-dev libxrender-dev
708
(libxinerama-dev)
392 by Marcin Wojdyr
minor doc updates
709
(glut.m4 wants libxmu-dev)
320 by Marcin Wojdyr
more coot dependencies
710
-->
329 by Marcin Wojdyr
ccp4.xml: added guile-gtk, guile-gui, oldssm
711
  <repository type="tarball" name="mrc_coot"
428 by Marcin Wojdyr
coot: updated URL, added --includedir
712
              href="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
713
  <custom id="coot-reference-structures"
714
          install_to="* share/coot/reference-structures/">
329 by Marcin Wojdyr
ccp4.xml: added guile-gtk, guile-gui, oldssm
715
    <branch repo="mrc_coot" module="dependencies/reference-structures.tar.gz"
716
            version="0" size="6728787"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
717
  </custom>
329 by Marcin Wojdyr
ccp4.xml: added guile-gtk, guile-gui, oldssm
718
  <autotools id="guile-gui">
719
    <branch repo="mrc_coot" module="dependencies/guile-gui-0.3.tar.gz"
720
            version="0.3" size="68535"/>
721
    <dependencies>
722
      <dep package="guile-gtk"/>
723
    </dependencies>
724
  </autotools>
725
333 by Marcin Wojdyr
ccp4.xml: another pango flag and added non-working module greg
726
  <!-- not really needed, nor working -->
727
  <autotools id="greg">
728
    <branch repo="mrc_coot" module="dependencies/greg-2.0.0-pe.tar.gz"
729
            version="2.0.0" size="453770"/>
730
    <dependencies>
731
      <dep package="guile"/>
732
    </dependencies>
733
  </autotools>
734
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
735
  <autotools id="coot" autogen-sh="configure"
1257 by Charles Ballard
added -lDistGeomHelpers to coot build
736
             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='-lDescriptors -lSubgraphs -lPartialCharges -lForceFieldHelpers -lForceField -lMolChemicalFeatures -lSubstructMatch -lOptimizer -lDepictor -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDistGeomHelpers -lDataStructs -lRDGeneral -lboost_python -lpython2.7' COOT_BUILD_INFO_STRING='CCP4, Oxfordshire'">
832 by Marcin Wojdyr
add coot prerelease, for now as coot-0.8
737
    <branch repo="mrc_coot"
1249 by Charles Ballard
update coot version to 0.8.8
738
            module="source/releases/coot-${version}.tar.gz"
739
            checkoutdir="coot-${version}" size="19472776" version="0.8.8">
887 by Marcin Wojdyr
updated coot
740
      <patch file="coot-coot-in.patch" strip="0" />
832 by Marcin Wojdyr
add coot prerelease, for now as coot-0.8
741
      <patch file="coot-syminfo.patch" strip="0" />
834 by Marcin Wojdyr
updated coot-0.8
742
      <patch file="coot-main-title.patch" strip="0"/>
1109 by Marcin Wojdyr
patch coot to make it work with RDKit 2015.03
743
      <patch file="coot-unfog-bitmap.patch" strip="0"/>
1216 by Charles Ballard
update for coot 0.8.6
744
      <patch file="coot-view.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"
988 by Marcin Wojdyr
tcltk84: build it out-of-source, make it use $LDFLAGS on Linux
776
            version="8.4.20.3" size="17833192">
514 by Charles Ballard
wrong strip level on patch
777
      <patch file="tcltk84-configure.patch" strip="0" />
324 by Marcin Wojdyr
updated coot version
778
    </branch>
779
  </custom>
780
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
781
  <repository type="tarball" name="cmake" href="http://www.cmake.org/files/"/>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
782
  <autotools id="cmake"
783
             autogen-template="%(srcdir)s/bootstrap --prefix=%(prefix)s">
1044 by Marcin Wojdyr
update cmake to 3.1.3
784
    <branch module="v3.1/cmake-${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=${prefix}">
1245 by Charles Ballard
update RDKit to 2016_09_04
817
    <branch module="rdkit/rdkit/archive/Release_${version}.tar.gz"
818
            repo="github-zip" version="2016_09_4" size="26887583"
1097 by Marcin Wojdyr
update RDKit
819
            checkoutdir="rdkit-Release_${version}">
1147 by Charles Ballard
patch for rdkit 2015_03_01 as mingw already has timezone defined
820
      <patch file="rdkit-DebugTrace-mingw.patch" strip="0" />
334 by Marcin Wojdyr
ccp4.xml: added rdkit
821
    </branch>
821 by Marcin Wojdyr
ccp4.xml: update rdkit
822
    <dependencies>
823
      <dep package="boost"/>
824
      <dep package="numpy"/>
825
      <dep package="sqlite3"/>
826
    </dependencies>
334 by Marcin Wojdyr
ccp4.xml: added rdkit
827
  </cmake>
828
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
829
  <repository type="tarball" name="bitbucket" href="https://bitbucket.org/"/>
830
  <autotools id="libgd" autogen-sh="configure"
1146 by Marcin Wojdyr
libgd: update 2.1.0 -> 2.1.1 and add option --without-vpx
831
             autogenargs="--with-png --with-jpeg --with-freetype --without-tiff --without-xpm --without-vpx --bindir=${prefix}/devbin">
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
832
    <branch repo="bitbucket"
331 by Marcin Wojdyr
updated libgd and python, added patch for coot
833
            module="libgd/gd-libgd/downloads/libgd-${version}.tar.bz2"
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
834
            checkoutdir="libgd-${version}"
1146 by Marcin Wojdyr
libgd: update 2.1.0 -> 2.1.1 and add option --without-vpx
835
            version="2.1.1" size="2308977">
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
836
    </branch>
837
    <dependencies>
838
      <dep package="libpng"/>
839
      <dep package="libjpeg"/>
840
    </dependencies>
403 by Marcin Wojdyr
ccp4.xml: add pkgconf to ccp4-windows
841
    <after>
842
      <dep package="pkgconf"/>
547 by Marcin Wojdyr
ccp4.xml: cosmetic changes
843
      <dep package="freetype2"/>
403 by Marcin Wojdyr
ccp4.xml: add pkgconf to ccp4-windows
844
    </after>
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
845
  </autotools>
306 by Marcin Wojdyr
added more coot dependencies
846
752 by Marcin Wojdyr
add sqlite3 (for Linux)
847
  <repository type="tarball" name="sqlite" href="http://sqlite.org/"/>
848
  <autotools id="sqlite3"
849
     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
850
    <branch repo="sqlite" module="2015/sqlite-autoconf-3081101.tar.gz"
851
            version="3.8.11.1" size="2101885"/>
752 by Marcin Wojdyr
add sqlite3 (for Linux)
852
  </autotools>
853
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
854
  <repository type="tarball" name="python"
855
              href="http://www.python.org/ftp/python/"/>
455 by Marcin Wojdyr
introduced directory devbin/ for binaries not needed after bulding is done
856
  <autotools id="python" autogenargs="--bindir=${prefix}/libexec">
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
857
    <pkg-config>python-2.7.pc</pkg-config>
1191 by Marcin Wojdyr
update python to 2.7.11
858
    <branch module="2.7.11/Python-2.7.11.tgz"
859
            repo="python" version="2.7.11" size="16856409">
591 by Charles Ballard
patch python build on os x
860
      <patch file="python-2.7.6-osx.patch" strip="0" />
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
861
    </branch>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
862
    <dependencies>
863
      <dep package="zlib"/>
864
      <dep package="bzip2"/>
865
      <dep package="openssl"/>
752 by Marcin Wojdyr
add sqlite3 (for Linux)
866
      <dep package="sqlite3"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
867
    </dependencies>
1278 by Colin Palmer
Add readline as a soft dependency for python
868
    <suggests>
869
      <dep package="readline"/>
870
    </suggests>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
871
  </autotools>
872
112 by Marcin Wojdyr
updated moduleset (zlib and refmac-dictionary)
873
  <cmake id="zlib">
308 by Marcin Wojdyr
ccp4.xml: update zlib
874
    <!-- both dynamic and static libraries are built -->
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
875
    <pkg-config>zlib.pc</pkg-config>
308 by Marcin Wojdyr
ccp4.xml: update zlib
876
    <branch repo="sf" module="libpng/zlib-1.2.8.tar.gz"
877
            version="1.2.8" size="571091"/>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
878
  </cmake>
879
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
880
  <repository type="tarball" name="sbrabec"
881
              href="http://ftp.suse.com/pub/people/sbrabec/"/>
455 by Marcin Wojdyr
introduced directory devbin/ for binaries not needed after bulding is done
882
  <autotools id="bzip2" autogenargs="--bindir=${prefix}/devbin">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
883
    <pkg-config>bzip2.pc</pkg-config>
884
    <!-- using autotool-ized tarball from Suse -->
885
    <branch repo="sbrabec" module="bzip2/tarballs/bzip2-1.0.6.0.1.tar.gz"
886
            version="1.0.6" size="1071724">
887
    </branch>
888
  </autotools>
889
890
  <repository type="tarball" name="openssl"
1226 by Marcin Wojdyr
update openssl as requested by Martyn, the old version is no longer on ftp
891
              href="https://www.openssl.org/source/"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
892
  <custom id="openssl"
888 by Marcin Wojdyr
ccp4.xml: updating openssl, hoping it will fix build problem on windows
893
          configure="./config --prefix=${prefix} --openssldir=${prefix}/etc/openssl no-hw shared"
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
894
          build="make" clean="make clean"
637 by Marcin Wojdyr
ccp4.xml, openssl: skip building docs (it fails with new pod2html)
895
          install="touch install_docs; make INSTALL_PREFIX=${destdir} install">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
896
    <pkg-config>openssl.pc</pkg-config>
897
    <branch repo="openssl" module="openssl-${version}.tar.gz"
1226 by Marcin Wojdyr
update openssl as requested by Martyn, the old version is no longer on ftp
898
            version="1.0.2j" size="5307912">
987 by Marcin Wojdyr
update openssl + patch for linking libgost.so
899
     <patch file="openssl-ldflags.patch" strip="0" />
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
900
    </branch>
901
    <dependencies>
902
      <dep package="zlib"/>
903
    </dependencies>
904
  </custom>
905
906
  <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
907
  <autotools id="curl" autogenargs="--disable-manual --disable-ldap --bindir=${prefix}/devbin">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
908
    <pkg-config>libcurl.pc</pkg-config>
909
    <branch module="curl-${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
910
            repo="curl" version="7.37.1" size="4076296">
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
911
     <patch file="curl-configure.patch" strip="0" />
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
912
    </branch>
319 by Marcin Wojdyr
ccp4.xml: more coot dependencies
913
    <dependencies>
914
      <dep package="openssl"/>
915
    </dependencies>
916
  </autotools>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
917
918
  <repository type="tarball" name="gnu" href="ftp://ftp.gnu.org/"/>
920 by Marcin Wojdyr
update gsl
919
  <!-- MINGW=true is a hack to link gsl with gslcblas and avoid problems
920
       when programs are linked with -as-needed -->
921
  <autotools id="gsl" autogenargs="MINGW=true">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
922
    <pkg-config>gsl.pc</pkg-config>
923
    <branch repo="gnu" module="gnu/gsl/gsl-${version}.tar.gz"
920 by Marcin Wojdyr
update gsl
924
            version="1.16" size="3534080"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
925
  </autotools>
926
329 by Marcin Wojdyr
ccp4.xml: added guile-gtk, guile-gui, oldssm
927
  <autotools id="guile-gtk" autogenargs="--without-glade --without-gtkgl">
928
    <branch repo="gnu" module="gnu/guile-gtk/guile-gtk-2.1.tar.gz"
929
            version="2.1" size="781985"/>
930
    <dependencies>
931
      <dep package="guile"/>
932
      <dep package="gtk2"/>
933
    </dependencies>
934
  </autotools>
935
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
936
  <repository type="tarball" name="gnome"
477 by Marcin Wojdyr
changed gnome download URL (the previous one didn't work with curl on OSX)
937
              href="http://ftp.gnome.org/pub/gnome/sources/"/>
306 by Marcin Wojdyr
added more coot dependencies
938
  <autotools id="libgnomecanvas" autogen-sh="configure" autogenargs="">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
939
    <pkg-config>libgnomecanvas-2.0.pc</pkg-config>
940
    <branch repo="gnome"
941
            module="libgnomecanvas/2.30/libgnomecanvas-${version}.tar.bz2"
942
            version="2.30.3" size="574139"/>
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
943
    <!--branch repo="gnome"
944
            module="libgnomecanvas/2.20/libgnomecanvas-${version}.tar.bz2"
945
            version="2.20.1" size="583613"/-->
319 by Marcin Wojdyr
ccp4.xml: more coot dependencies
946
    <dependencies>
947
      <dep package="gtk2"/>
948
      <dep package="libart_lgpl"/>
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
949
      <!--dep package="libglade"/-->
319 by Marcin Wojdyr
ccp4.xml: more coot dependencies
950
    </dependencies>
951
  </autotools>
952
  <autotools id="libart_lgpl" autogen-sh="configure" autogenargs="">
953
    <branch repo="gnome"
954
            module="libart_lgpl/2.3/libart_lgpl-${version}.tar.bz2"
955
            version="2.3.21" size="329102"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
956
  </autotools>
884 by Marcin Wojdyr
ccp4.xml: goocanvas: "make" only in src, to avoid problem with linking demos
957
  <autotools id="goocanvas" autogen-sh="configure" autogenargs=""
958
             makeargs="SUBDIRS=src"
959
             makeinstallargs="SUBDIRS=src install">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
960
    <pkg-config>goocanvas.pc</pkg-config>
961
    <branch repo="gnome" module="goocanvas/1.0/goocanvas-1.0.0.tar.bz2"
962
            version="1.0.0" size="570552"/>
317 by Marcin Wojdyr
minor updates
963
    <dependencies>
964
      <dep package="gtk2"/>
965
      <dep package="cairo"/>
966
    </dependencies>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
967
  </autotools>
968
  <autotools id="pygtk" autogenargs="--without-glade">
969
    <branch repo="gnome" module="pygtk/2.24/pygtk-2.24.0.tar.bz2"
970
            version="2.24.0" size="2361097"/>
971
    <dependencies>
972
      <dep package="pygobject2"/>
973
      <dep package="py2cairo"/>
974
    </dependencies>
975
  </autotools>
976
  <autotools id="pygobject2" autogenargs="--disable-introspection">
977
    <branch repo="gnome" module="pygobject/2.28/pygobject-2.28.6.tar.bz2"
978
            version="2.28.6" size="888240"/>
322 by Marcin Wojdyr
adding dependencies, patch for libffi
979
    <dependencies>
980
      <dep package="glib"/>
981
      <dep package="py2cairo"/>
982
    </dependencies>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
983
  </autotools>
306 by Marcin Wojdyr
added more coot dependencies
984
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
985
  <repository type="tarball" name="cairo" href="http://cairographics.org/"/>
986 by Marcin Wojdyr
ccp4.xml: build cairo with --disable-trace (to make it simpler)
986
  <autotools id="cairo" autogen-sh="configure"
987
              autogenargs="--enable-xlib --disable-trace">
306 by Marcin Wojdyr
added more coot dependencies
988
    <pkg-config>cairo.pc</pkg-config>
989
    <!--
990
    <branch repo="cairo" module="releases/cairo-1.8.10.tar.gz"
991
            version="1.8.10" size="7102657"/>
992
    -->
993
    <branch repo="cairo" module="releases/cairo-1.10.2.tar.gz"
994
            version="1.10.2" size="23558405"/>
995
    <dependencies>
996
      <dep package="pixman"/>
320 by Marcin Wojdyr
more coot dependencies
997
      <dep package="libpng"/>
306 by Marcin Wojdyr
added more coot dependencies
998
    </dependencies>
894 by Marcin Wojdyr
ccp4.xml: cairo after freetype2
999
    <after>
1000
      <dep package="freetype2"/>
1001
    </after>
306 by Marcin Wojdyr
added more coot dependencies
1002
  </autotools>
1003
  <autotools id="pixman" autogen-sh="configure" autogenargs="--disable-gtk">
1004
    <branch repo="cairo" module="releases/pixman-0.28.2.tar.gz"
1005
            version="0.28.2" size="734094"/>
1006
    <dependencies>
1007
    </dependencies>
1008
  </autotools>
1009
839 by Marcin Wojdyr
ccp4.xml: added intltool
1010
  <autotools id="intltool" autogenargs="--bindir=${prefix}/devbin">
1011
    <branch repo="lp" module="intltool/trunk/0.50.2/+download/intltool-${version}.tar.gz"
1012
            version="0.50.2" size="189483"/>
1013
  </autotools>
1014
833 by Marcin Wojdyr
ccp4.xml: gettext: avoid checking for Java (and popup message on OSX)
1015
  <!-- only libintl.dylib is used by glib
1016
       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)
1017
  <autotools id="gettext"
833 by Marcin Wojdyr
ccp4.xml: gettext: avoid checking for Java (and popup message on OSX)
1018
   autogenargs="--bindir=${prefix}/devbin --disable-java --disable-libasprintf --disable-curses GCJ=none">
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
1019
    <branch repo="gnu" module="pub/gnu/gettext/gettext-${version}.tar.gz"
1020
            version="0.18.3.2" size="16189249"/>
1021
  </autotools>
1022
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1023
  <autotools id="py2cairo">
1024
    <branch repo="cairo" module="releases/pycairo-1.2.2.tar.gz"
306 by Marcin Wojdyr
added more coot dependencies
1025
            version="1.2.2" size="482417">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1026
    </branch>
306 by Marcin Wojdyr
added more coot dependencies
1027
    <dependencies>
1028
      <dep package="cairo"/>
1029
    </dependencies>
322 by Marcin Wojdyr
adding dependencies, patch for libffi
1030
    <after>
1031
      <dep package="python"/>
1032
    </after>
306 by Marcin Wojdyr
added more coot dependencies
1033
  </autotools>
1034
817 by Marcin Wojdyr
ccp4.xml: glib: disable dtrace because of https://trac.macports.org/ticket/30413
1035
  <autotools id="glib" autogenargs="--disable-modular-tests --disable-selinux --disable-dtrace ac_cv_func_splice=no">
306 by Marcin Wojdyr
added more coot dependencies
1036
    <pkg-config>glib-2.0.pc</pkg-config>
1037
    <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
1038
            version="2.34.3" size="6334872">
1039
      <patch file="glib-osx-gcc-fix.patch" strip="1" />
1040
    </branch>
306 by Marcin Wojdyr
added more coot dependencies
1041
    <dependencies>
320 by Marcin Wojdyr
more coot dependencies
1042
      <dep package="libffi"/>
866 by Marcin Wojdyr
ccpem dependency changed from mmdb to mmdb2
1043
      <dep package="gettext"/> <!-- skipped by default on non-OSX -->
320 by Marcin Wojdyr
more coot dependencies
1044
    </dependencies>
1045
  </autotools>
1046
835 by Marcin Wojdyr
updated cctbx-phaser to the version from 2014-05-07
1047
  <!-- ver. 3.1 has a new problem in libffi.pc.
1048
       configure patch will stay anyway to avoid ../lib64 -->
320 by Marcin Wojdyr
more coot dependencies
1049
  <repository type="tarball" name="sourceware"
1050
              href="ftp://sourceware.org/pub/"/>
1051
  <autotools id="libffi" autogenargs="--enable-portable-binary">
1052
    <pkg-config>libffi.pc</pkg-config>
1053
    <branch repo="sourceware" module="libffi/libffi-${version}.tar.gz"
322 by Marcin Wojdyr
adding dependencies, patch for libffi
1054
            version="3.0.13" size="845747">
1055
      <patch file="libffi-configure.patch" strip="1" />
769 by Charles Ballard
intel compier int128 problem pre icc 13 in libffi
1056
      <patch file="libffi_intel_define.patch" strip="0" />
322 by Marcin Wojdyr
adding dependencies, patch for libffi
1057
    </branch>
306 by Marcin Wojdyr
added more coot dependencies
1058
  </autotools>
1059
1060
  <!-- pango 1.23 requires fontconfig >= 2.5 (not on CentOS 5) -->
361 by Marcin Wojdyr
added triggers/, adjusted ccp4.xml
1061
  <!-- with included-modules there is no need to call pango-querymodules -->
306 by Marcin Wojdyr
added more coot dependencies
1062
  <autotools id="pango" autogen-sh="configure"
333 by Marcin Wojdyr
ccp4.xml: another pango flag and added non-working module greg
1063
             autogenargs="--disable-introspection --with-included-modules">
306 by Marcin Wojdyr
added more coot dependencies
1064
    <pkg-config>pango.pc</pkg-config>
1065
    <branch repo="gnome" module="pango/1.22/pango-1.22.4.tar.bz2"
1066
            version="1.22.4" size="1496168"/>
1067
    <dependencies>
1068
      <dep package="cairo"/>
486 by Marcin Wojdyr
ccp4.xml: pango requires glib
1069
      <dep package="glib"/>
306 by Marcin Wojdyr
added more coot dependencies
1070
      <!-- <dep package="harfbuzz"/> -->
1071
    </dependencies>
1072
  </autotools>
319 by Marcin Wojdyr
ccp4.xml: more coot dependencies
1073
  <autotools id="pangox" autogen-sh="configure">
1074
    <pkg-config>pangox.pc</pkg-config>
1075
    <branch repo="gnome" module="pangox-compat/0.0/pangox-compat-0.0.2.tar.xz"
1076
            version="0.0.2" size="267396"/>
1077
    <dependencies>
1078
      <dep package="pango"/>
1079
    </dependencies>
1080
  </autotools>
306 by Marcin Wojdyr
added more coot dependencies
1081
1082
  <repository type="tarball" name="freedesktop"
1083
               href="http://www.freedesktop.org/software/"/>
1084
  <autotools id="harfbuzz" autogen-sh="configure">
1085
    <pkg-config>harfbuzz.pc</pkg-config>
1086
    <branch repo="freedesktop"
1087
            module="harfbuzz/release/harfbuzz-0.9.16.tar.bz2"
1088
            version="0.9.16" size="902208"/>
1089
    <dependencies>
1090
      <dep package="glib"/>
1091
      <dep package="libicu"/>
1092
    </dependencies>
1093
  </autotools>
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
1094
  <autotools id="fontconfig" autogen-sh="configure" autogenargs="">
1095
    <pkg-config>fontconfig.pc</pkg-config>
1096
    <branch repo="freedesktop" module="fontconfig/release/fontconfig-${version}.tar.gz"
1097
            version="2.10.1" size="1700168"/>
1098
    <dependencies>
1099
      <!--<dep package="iconv"/>-->
1100
      <!--<dep package="expat"/>-->
1101
    </dependencies>
1102
  </autotools>
306 by Marcin Wojdyr
added more coot dependencies
1103
1104
  <repository type="tarball" name="icu"
1105
              href="http://download.icu-project.org/files/"/>
1106
  <autotools id="libicu" autogen-sh="source/configure"
1107
             autogenargs="--disable-tests --disable-samples --disable-rpath">
1108
    <pkg-config>icu-i18n.pc</pkg-config>
1109
    <branch repo="icu" module="icu4c/51.1/icu4c-51_1-src.tgz"
1110
            checkoutdir="libicu-51.1" version="51.1" size="21815174"/>
1111
  </autotools>
1112
1113
  <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
1114
             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
1115
    <branch repo="gnome" module="gdk-pixbuf/2.28/gdk-pixbuf-2.28.1.tar.xz"
335 by Marcin Wojdyr
added gdk-pixbuf-hack.patch
1116
            version="2.28.1" size="1191084">
1117
      <patch file="gdk-pixbuf-hack.patch" strip="0" />
1118
    </branch>
306 by Marcin Wojdyr
added more coot dependencies
1119
    <dependencies>
1120
      <dep package="libpng"/>
1121
      <dep package="libjpeg"/>
1122
      <dep package="glib"/>
1123
    </dependencies>
1124
  </autotools>
1125
1126
  <autotools id="librsvg" autogen-sh="configure"
1127
             autogenargs="--disable-introspection --disable-gtk-theme --disable-tools --disable-vala">
1128
    <!--
1129
    <branch repo="gnome" module="librsvg/2.36/librsvg-${version}.tar.xz"
1130
            version="2.36.4" size="513028"/>
1131
    -->
1132
    <branch repo="gnome" module="librsvg/2.32/librsvg-2.32.1.tar.bz2"
1133
            version="2.32.1" size="517170"/>
1134
    <dependencies>
1135
      <dep package="gdk-pixbuf"/>
1136
      <dep package="libcroco"/>
1137
    </dependencies>
1138
  </autotools>
325 by Marcin Wojdyr
workaround for libcroco -Wl,-Bsymbolic-functions error
1139
  <autotools id="libcroco" autogen-sh="configure"
1140
             autogenargs="--enable-Bsymbolic=auto">
1155 by Marcin Wojdyr
update libcroco 0.6.8 to 0.6.11
1141
    <branch repo="gnome" module="libcroco/0.6/libcroco-0.6.11.tar.xz"
1142
            version="0.6.11" size="477312"/>
306 by Marcin Wojdyr
added more coot dependencies
1143
    <dependencies>
1144
      <dep package="glib"/>
1145
      <dep package="libxml2"/>
1146
      <dep package="pango"/>
1147
    </dependencies>
1148
  </autotools>
1149
1150
  <autotools id="atk" autogen-sh="configure"
1151
             autogenargs="--disable-introspection --disable-glibtest">
1152
    <branch repo="gnome" module="atk/2.8/atk-2.8.0.tar.xz"
1153
            version="2.8.0" size="634052"/>
1154
    <dependencies>
1155
      <dep package="glib"/>
1156
    </dependencies>
1157
  </autotools>
1158
1159
  <autotools id="gtk2" autogen-sh="configure"
770 by Charles Ballard
gtk2: for none gcc compilers the visibility is a problem
1160
             autogenargs="--disable-visibility --disable-introspection --disable-glibtest --disable-cups --disable-papi --with-included-immodules">
1099 by Marcin Wojdyr
update gtk 2.24.23 to 2.24.28
1161
    <branch repo="gnome" module="gtk+/2.24/gtk+-${version}.tar.xz"
1162
            version="2.24.28" size="13354884"/>
306 by Marcin Wojdyr
added more coot dependencies
1163
    <dependencies>
1164
      <dep package="glib"/>
1165
      <dep package="cairo"/>
1166
      <dep package="pango"/>
1167
      <dep package="atk"/>
1168
      <dep package="gdk-pixbuf"/>
1169
    </dependencies>
1170
  </autotools>
361 by Marcin Wojdyr
added triggers/, adjusted ccp4.xml
1171
306 by Marcin Wojdyr
added more coot dependencies
1172
  <autotools id="gtkglext" autogen-sh="configure"
1173
             autogenargs="--disable-introspection --disable-glibtest">
319 by Marcin Wojdyr
ccp4.xml: more coot dependencies
1174
    <branch repo="gnome" module="gtkglext/1.2/gtkglext-1.2.0.tar.bz2"
1175
            version="1.2.0" size="703821">
1176
      <patch file="gtkglext-1.2.0-bz677457.diff" strip="1" />
1177
    </branch>
306 by Marcin Wojdyr
added more coot dependencies
1178
    <dependencies>
1179
      <dep package="gtk2"/>
1190 by Marcin Wojdyr
pango and pangox-compat install the same files
1180
      <dep package="pango"/>
306 by Marcin Wojdyr
added more coot dependencies
1181
    </dependencies>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1182
  </autotools>
1183
342 by Marcin Wojdyr
ccp4.xml: added libglade
1184
  <autotools id="libglade"
1185
     autogenargs="--disable-gtktest CPPFLAGS=&quot;$CPPFLAGS -UG_DISABLE_DEPRECATED&quot; --with-xml-catalog=/dev/null">
1186
    <pkg-config>libglade-2.0.pc</pkg-config>
1187
    <branch repo="gnome" module="libglade/2.6/libglade-2.6.4.tar.bz2"
1188
            version="2.6.4" size="356119"/>
1189
    <dependencies>
1190
      <dep package="gtk2"/>
1191
      <dep package="gdk-pixbuf"/>
1192
      <dep package="libxml2"/>
1193
    </dependencies>
1194
  </autotools>
1195
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1196
  <autotools id="guile" autogenargs="--disable-rpath --disable-error-on-warning">
1197
    <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
1198
            version="1.8.8" size="3956654">
576 by Ville Uski
Add '/' on line 943 in ccp4.xml to correct a syntax error
1199
      <patch file="guile-configure.patch" strip="0"/>
808 by Marcin Wojdyr
added guile-fink.patch
1200
      <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
1201
    </branch>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1202
    <dependencies>
1203
      <dep package="libtool"/>
320 by Marcin Wojdyr
more coot dependencies
1204
      <dep package="gmp"/>
811 by Marcin Wojdyr
ccp4.xml: add readline as guile dependency
1205
      <dep package="readline"/>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1206
    </dependencies>
1207
  </autotools>
341 by Marcin Wojdyr
ccp4.xml: configure gmp with --disable-assembly (should be more portable
1208
  <autotools id="gmp" autogenargs="--disable-assembly">
320 by Marcin Wojdyr
more coot dependencies
1209
    <branch repo="gnu" module="gnu/gmp/gmp-5.1.1.tar.bz2"
1210
            version="5.1.1" size="2213841"/>
1211
  </autotools>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1212
  <autotools id="libtool" autogenargs="">
1213
    <branch repo="gnu" module="gnu/libtool/libtool-2.4.tar.gz"
1214
            version="2.4" size="2580417"/>
1215
  </autotools>
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
1216
  <autotools id="readline" autogenargs="">
1217
    <branch repo="gnu" module="gnu/readline/readline-${version}.tar.gz"
1261 by Tom Burnley
remove qtrview from ccpem deps
1218
            version="7.0" size="2910016">
812 by Marcin Wojdyr
added a patch to readline to remove -arch_only on OSX
1219
      <patch file="readline-shobj-conf.patch" strip="0"/>
1220
    </branch>
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
1221
  </autotools>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1222
1223
  <repository type="tarball" name="savannah"
1224
              href="http://download.savannah.gnu.org/releases/"/>
1225
  <autotools id="guile-lib">
1237 by Tom Burnley
update guile repo
1226
    <branch repo="savannah" module="guile-lib/old/guile-lib-0.2.2.tar.gz"
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1227
            version="0.2.2" size="476723"/>
1228
    <dependencies>
1229
      <dep package="guile"/>
1230
    </dependencies>
1231
  </autotools>
1232
353 by Marcin Wojdyr
ccp4.xml: added freetype2
1233
  <autotools id="freetype2">
1234
    <pkg-config>freetype2.pc</pkg-config>
1209 by Marcin Wojdyr
take freetype from SF instead of Savannah, because:
1235
    <branch repo="sf" module="freetype/freetype-${version}.tar.bz2"
1192 by Marcin Wojdyr
minor freetype update 2.5.3 -> 2.5.5
1236
            version="2.5.5" size="1714529"/>
353 by Marcin Wojdyr
ccp4.xml: added freetype2
1237
  </autotools>
1238
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1239
  <repository type="tarball" name="pypi"
1240
              href="https://pypi.python.org/packages/source/"/>
931 by Marcin Wojdyr
ccp4.xml: add --install-scripts=${prefix}/libexec for easyinstall, pip, bzr
1241
  <distutils id="setuptools" installargs="--install-scripts=${prefix}/libexec">
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1242
    <branch repo="pypi" module="s/setuptools/setuptools-${version}.tar.gz"
613 by Marcin Wojdyr
ccp4.xml: added more ccp4mg dependencies: suds, lxml, libxslt,
1243
            version="2.0" size="783643" />
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1244
    <dependencies/>
322 by Marcin Wojdyr
adding dependencies, patch for libffi
1245
    <after>
1246
      <dep package="python"/>
1247
    </after>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1248
  </distutils>
931 by Marcin Wojdyr
ccp4.xml: add --install-scripts=${prefix}/libexec for easyinstall, pip, bzr
1249
  <distutils id="pip" installargs="--install-scripts=${prefix}/libexec">
613 by Marcin Wojdyr
ccp4.xml: added more ccp4mg dependencies: suds, lxml, libxslt,
1250
    <branch repo="pypi" module="p/pip/pip-${version}.tar.gz"
993 by Marcin Wojdyr
ccp4.xml: updated pip, hopefully this will resolve some proxy issues
1251
            version="1.5.6" size="938120" />
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1252
    <dependencies/>
322 by Marcin Wojdyr
adding dependencies, patch for libffi
1253
    <after>
1254
      <dep package="python"/>
1255
    </after>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1256
  </distutils>
1257
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1258
  <distutils id="numpy">
1258 by Tom Burnley
move to numpy 1.12.1
1259
    <branch repo="pypi" module="../a5/16/8a678404411842fe02d780b5f0a676ff4d79cd58f0f22acddab1b392e230/numpy-${version}.zip"
1260
            version="1.12.1">
1264 by Charles Ballard
activate numpy patch for intel compilers
1261
      <patch file="numpy-intelcompiler.patch" strip="0"/>
1137 by Charles Ballard
add patch for numpy distutils intel compiler on darwin
1262
    </branch>
754 by Marcin Wojdyr
add missing dependecies
1263
    <dependencies>
1262 by Tom Burnley
add setuptools dep for numpy
1264
      <dep package="setuptools"/>
754 by Marcin Wojdyr
add missing dependecies
1265
      <dep package="lapack"/>
1266
    </dependencies>
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1267
    <after>
1268
      <dep package="python"/>
1269
    </after>
1270
  </distutils>
1271
1118 by Marcin Wojdyr
add scipy
1272
  <distutils id="scipy">
1273
    <branch repo="pypi" module="s/scipy/scipy-${version}.tar.gz"
1159 by Marcin Wojdyr
update numpy & scipy
1274
            version="0.16.1" size="12221561" />
1118 by Marcin Wojdyr
add scipy
1275
    <dependencies>
1276
      <dep package="numpy"/>
1277
    </dependencies>
1278
  </distutils>
1279
1289 by Tom Burnley
add mpi4py, return coot to ccpem
1280
  <distutils id="mpi4py">
1281
    <branch repo="pypi" module="../ee/b8/f443e1de0b6495479fc73c5863b7b5272a4ece5122e3589db6cd3bb57eeb/mpi4py-${version}.tar.gz"
1282
            version="2.0.0"/>
1283
    <dependencies>
1284
      <dep package="numpy"/>
1285
      <dep package="scipy"/>
1293 by Tom Burnley
revert ccpem deps for standard qt4 build
1286
      <dep package="openmpi"/>
1289 by Tom Burnley
add mpi4py, return coot to ccpem
1287
    </dependencies>
1288
  </distutils>
1289
1290
<!--https://pypi.python.org/packages/ee/b8/f443e1de0b6495479fc73c5863b7b5272a4ece5122e3589db6cd3bb57eeb/mpi4py-2.0.0.tar.gz#md5=4f7d8126d7367c239fd67615680990e3-->
1291
1175 by Marcin Wojdyr
add pandas
1292
  <distutils id="pandas">
1293
    <branch repo="pypi" module="p/pandas/pandas-${version}.tar.gz"
1294
            version="0.17.1" size="6674479" />
1295
    <dependencies>
1296
      <dep package="numpy"/>
1297
      <dep package="python-dateutil"/>
1177 by Marcin Wojdyr
adding pytz - required by pandas
1298
      <dep package="pytz"/>
1175 by Marcin Wojdyr
add pandas
1299
    </dependencies>
1300
  </distutils>
1301
967 by Marcin Wojdyr
ccp4.xml: added biopython
1302
  <distutils id="biopython">
1303
    <branch repo="pypi" module="b/biopython/biopython-${version}.tar.gz"
1102 by Marcin Wojdyr
updated biopython
1304
            version="1.65" size="12641382" />
967 by Marcin Wojdyr
ccp4.xml: added biopython
1305
    <dependencies>
1306
      <dep package="numpy"/>
1307
    </dependencies>
1308
  </distutils>
1309
1061 by Marcin Wojdyr
add PyCrypto (for arcimboldo)
1310
  <distutils id="pycrypto">
1311
    <branch repo="pypi" module="p/pycrypto/pycrypto-${version}.tar.gz"
1312
            version="2.6.1" size="446240" />
1130 by Marcin Wojdyr
pycrypto depends on gmp
1313
    <dependencies>
1314
      <dep package="gmp"/>
1315
    </dependencies>
1115 by Marcin Wojdyr
add paramiko (for arcimboldo)
1316
    <after>
1317
      <dep package="python"/>
1318
    </after>
1061 by Marcin Wojdyr
add PyCrypto (for arcimboldo)
1319
  </distutils>
1320
990 by Marcin Wojdyr
ccp4.xml: added pillow
1321
  <distutils id="pillow">
1322
    <branch repo="pypi" module="P/Pillow/Pillow-${version}.tar.gz"
1323
            version="2.6.1" size="7321920" />
1324
    <dependencies>
1325
      <dep package="libjpeg"/>
1326
      <dep package="zlib"/>
1001 by Marcin Wojdyr
ccp4.xml fix wrong pillow dependency name
1327
      <dep package="tiff"/>
990 by Marcin Wojdyr
ccp4.xml: added pillow
1328
    </dependencies>
991 by Marcin Wojdyr
ccp4.xml: add setuptools to ccpem
1329
    <after>
1330
      <dep package="python"/>
1331
      <dep package="setuptools"/>
1332
    </after>
990 by Marcin Wojdyr
ccp4.xml: added pillow
1333
  </distutils>
1334
1115 by Marcin Wojdyr
add paramiko (for arcimboldo)
1335
  <distutils id="paramiko">
1336
    <branch repo="pypi" module="p/paramiko/paramiko-${version}.tar.gz"
1337
            version="1.15.2" size="1220578" />
1338
    <dependencies>
1339
      <dep package="pycrypto"/>
1340
    </dependencies>
1341
  </distutils>
1342
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1343
  <distutils id="python-dateutil">
1175 by Marcin Wojdyr
add pandas
1344
    <branch repo="pypi" module="p/python-dateutil/python-dateutil-2.4.2.tar.gz"
1345
            version="2.4.2" size="209120" />
1176 by Marcin Wojdyr
new python-dateutil depends on six
1346
    <dependencies>
1347
      <dep package="six"/>
1348
    </dependencies>
1349
    <after>
1350
      <dep package="python"/>
1351
      <dep package="setuptools"/>
1352
    </after>
1353
  </distutils>
1354
1177 by Marcin Wojdyr
adding pytz - required by pandas
1355
  <distutils id="pytz">
1356
    <branch repo="pypi" module="p/pytz/pytz-2015.7.tar.gz"
1357
            version="2015.7" size="282002" />
1358
    <after>
1359
      <dep package="python"/>
1360
      <dep package="setuptools"/>
1361
    </after>
1362
  </distutils>
1363
1176 by Marcin Wojdyr
new python-dateutil depends on six
1364
  <distutils id="six">
1365
    <branch repo="pypi" module="s/six/six-1.10.0.tar.gz"
1366
            version="1.10.0" size="29630" />
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1367
    <dependencies/>
1368
    <after>
1369
      <dep package="python"/>
1175 by Marcin Wojdyr
add pandas
1370
      <dep package="setuptools"/>
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1371
    </after>
1372
  </distutils>
1373
1374
  <distutils id="pyparsing">
1375
    <branch repo="pypi" module="p/pyparsing/pyparsing-2.0.1.tar.gz"
1376
            version="2.0.1" size="1129563" />
1377
    <dependencies/>
1378
    <after>
1379
      <dep package="python"/>
1380
    </after>
1381
  </distutils>
1382
1383
  <distutils id="matplotlib">
916 by Marcin Wojdyr
downgrade matplotlib to avoid dependency on newer freetype2
1384
    <!-- matplotlib 1.4 requires freetype2 2.4+, on RHEL5 it's 2.2.1 -->
1385
    <branch repo="pypi" module="m/matplotlib/matplotlib-${version}.tar.gz"
1193 by Marcin Wojdyr
update matplotlib as it doesn't build with the current numpy version
1386
            version="1.4.3" size="50413837">
708 by Marcin Wojdyr
matplotlib: don't install tests and sample-data
1387
      <patch file="matplotlib-setup-cfg.patch" strip="0"/>
1388
    </branch>
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1389
    <dependencies>
1193 by Marcin Wojdyr
update matplotlib as it doesn't build with the current numpy version
1390
       <dep package="freetype2"/>
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1391
       <dep package="numpy"/>
1392
       <dep package="python-dateutil"/>
1393
       <dep package="pyparsing"/>
910 by Marcin Wojdyr
updated numpy and matplotlib
1394
       <dep package="libpng"/>
934 by Marcin Wojdyr
ccp4.xml: add pyqt4 as dep of matplotlib
1395
       <dep package="pyqt4"/>
705 by Charles Ballard
add numpy, matplotlib, with some of the dependencies - as required by GUI2
1396
    </dependencies>
1397
    <after>
1398
      <dep package="python"/>
1399
    </after>
1400
  </distutils>
1401
1199 by Marcin Wojdyr
add MarkupSafe for PANDDA
1402
  <distutils id="markupsafe">
1403
    <branch repo="pypi" module="M/MarkupSafe/MarkupSafe-0.23.tar.gz"
1404
            version="0.23" size="13416" />
1405
    <dependencies/>
1406
    <after>
1407
      <dep package="python"/>
1408
    </after>
1409
  </distutils>
1410
1170 by Marcin Wojdyr
add jinja2
1411
  <distutils id="jinja2">
1412
    <branch repo="pypi" module="J/Jinja2/Jinja2-2.8.tar.gz"
1413
            version="2.8" size="357055" />
1414
    <dependencies/>
1415
    <after>
1416
      <dep package="python"/>
1417
    </after>
1418
  </distutils>
1419
1208 by Marcin Wojdyr
add a pytest dependency (for Tom B.)
1420
  <distutils id="py">
1273 by Tom Burnley
update py module to 1.4.34 for use with pytest 3.1.3
1421
    <branch repo="pypi" module="../68/35/58572278f1c097b403879c1e9369069633d1cbad5239b9057944bb764782/py-1.4.34.tar.gz"
1422
            version="1.4.34"/>
1208 by Marcin Wojdyr
add a pytest dependency (for Tom B.)
1423
    <dependencies/>
1424
    <after>
1425
      <dep package="python"/>
1426
    </after>
1427
  </distutils>
1272 by Tom Burnley
update version of pytest and xdist
1428
1207 by Marcin Wojdyr
add pytest and pytest-xdist for ccpem
1429
  <distutils id="pytest">
1272 by Tom Burnley
update version of pytest and xdist
1430
    <branch repo="pypi" module="../15/c8/6b42bf58f91d72416806472512bb67dabc6edb5a6a8ace29853ff940400a/pytest-3.1.3.tar.gz"
1431
            version="3.1.3"/>
1208 by Marcin Wojdyr
add a pytest dependency (for Tom B.)
1432
    <dependencies>
1433
      <dep package="py"/>
1272 by Tom Burnley
update version of pytest and xdist
1434
      <dep package="python"/>
1208 by Marcin Wojdyr
add a pytest dependency (for Tom B.)
1435
    </dependencies>
1207 by Marcin Wojdyr
add pytest and pytest-xdist for ccpem
1436
  </distutils>
1272 by Tom Burnley
update version of pytest and xdist
1437
1207 by Marcin Wojdyr
add pytest and pytest-xdist for ccpem
1438
  <distutils id="pytest-xdist">
1272 by Tom Burnley
update version of pytest and xdist
1439
    <branch repo="pypi" module="../90/03/1d6a1ab90f6cdfc62a36d93fc341db1384a97a24ed9c5ea0e4004d70c8a3/pytest-xdist-1.18.1.tar.gz"
1440
            version="1.18.1"/>
1207 by Marcin Wojdyr
add pytest and pytest-xdist for ccpem
1441
    <dependencies>
1442
      <dep package="pytest"/>
1268 by Tom Burnley
add execnet, dependancy of pytest-xdist
1443
      <dep package="execnet"/>
1207 by Marcin Wojdyr
add pytest and pytest-xdist for ccpem
1444
    </dependencies>
1445
  </distutils>
1446
1269 by Tom Burnley
add apipkg dep for execnet and pytest
1447
  <distutils id="apipkg">
1448
    <branch repo="pypi" module="../52/b7/046127821e93d8114338e9431ff896e3cf076e5e510c9ded4cf812af8de5/apipkg-1.2.zip"
1449
            version="1.2" />
1450
  </distutils>
1451
1268 by Tom Burnley
add execnet, dependancy of pytest-xdist
1452
  <distutils id="execnet">
1453
    <branch repo="pypi" module="../eb/ee/43729e7dee8772e69b3b01715ab9742790be2eace2d18cf53d219b9c31f8/execnet-1.4.1.tar.gz"
1454
            version="1.4.1" />
1455
    <dependencies/>
1456
    <after>
1457
      <dep package="python"/>
1269 by Tom Burnley
add apipkg dep for execnet and pytest
1458
      <dep package="apipkg"/>
1268 by Tom Burnley
add execnet, dependancy of pytest-xdist
1459
    </after>
1460
  </distutils>
1461
1265 by Charles Ballard
add setuptools-scm, which may be required to get around pip issues in installing pytest-xdist
1462
  <distutils id="setuptools-scm">
1463
    <branch repo="pypi" version="1.15.0" size="23677"
1464
            module="../80/b7/31b6ae5fcb188e37f7e31abe75f9be90490a5456a72860fa6e643f8a3cbc/setuptools_scm-1.15.0.tar.gz"/>
1465
    <after>
1466
      <dep package="python"/>
1467
      <dep package="setuptools"/>
1468
    </after>
1469
  </distutils>
1470
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1471
  <repository type="tarball" name="lp" href="https://launchpad.net/"/>
931 by Marcin Wojdyr
ccp4.xml: add --install-scripts=${prefix}/libexec for easyinstall, pip, bzr
1472
  <distutils id="bzr" installargs="--install-scripts=${prefix}/libexec">
487 by Marcin Wojdyr
ccp4.xml: updated bzr
1473
    <branch repo="lp" module="bzr/2.6/2.6.0/+download/bzr-2.6.0.tar.gz"
1474
            version="2.6.0" size="11301124" />
322 by Marcin Wojdyr
adding dependencies, patch for libffi
1475
    <after>
1476
      <dep package="python"/>
1477
    </after>
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1478
  </distutils>
1479
1288 by Charles Ballard
update location and version of hdf5, synch requirement to dials 1.7.2
1480
  <repository type="tarball" name="hdf5" href="https://support.hdfgroup.org/ftp/"/>
1075 by Marcin Wojdyr
update hdf5
1481
  <cmake id="hdf5"
1288 by Charles Ballard
update location and version of hdf5, synch requirement to dials 1.7.2
1482
      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
1483
    <branch repo="hdf5"
1288 by Charles Ballard
update location and version of hdf5, synch requirement to dials 1.7.2
1484
            module="HDF5/releases/hdf5-1.10/hdf5-${version}/src/hdf5-${version}.tar.gz"
1485
            version="1.10.0-patch1" size="14007792"/>
942 by Marcin Wojdyr
ccp4.xml: added hdf5
1486
    <dependencies>
1487
      <dep package="zlib"/>
1488
    </dependencies>
962 by Marcin Wojdyr
ccp4.xml: change hdf5 build to cmake - the only way to build it on Windows
1489
  </cmake>
942 by Marcin Wojdyr
ccp4.xml: added hdf5
1490
1491
  <distutils id="h5py">
1492
    <branch repo="pypi" module="h/h5py/h5py-${version}.tar.gz"
1493
            version="2.3.1" size="1072766"/>
1494
    <dependencies>
1495
      <dep package="hdf5"/>
1496
      <dep package="numpy"/>
1497
    </dependencies>
1498
  </distutils>
1499
1139 by Andrey Lebedev
arcimboldo is now build from sources; added ecdsa module
1500
  <distutils id="ecdsa">
1501
    <branch repo="pypi" module="e/ecdsa/ecdsa-${version}.tar.gz"
1502
            version="0.13" size="55579"/>
1503
    <dependencies/>
1504
  </distutils>
1505
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1506
  <repository type="tarball" name="xmlsoft.org" href="ftp://xmlsoft.org/"/>
455 by Marcin Wojdyr
introduced directory devbin/ for binaries not needed after bulding is done
1507
  <autotools id="libxml2" autogenargs="--without-python --without-threads --with-zlib --bindir=${prefix}/devbin">
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1508
    <pkg-config>libxml-2.0.pc</pkg-config>
407 by Marcin Wojdyr
updated libxml2 to 2.9.1
1509
    <branch module="libxml2/libxml2-${version}.tar.gz"
1295 by Tom Burnley
update libxml2 version
1510
            repo="xmlsoft.org" version="2.9.6"/>
405 by Marcin Wojdyr
ccp4.xml: add zlib dependency to libxml2 (it doesn't really build w/o zlib)
1511
    <dependencies>
1512
      <dep package="zlib"/>
1513
    </dependencies>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1514
  </autotools>
696 by Marcin Wojdyr
ccp4.xml: libxslt on Windows comment
1515
  <!-- on Windows patched using: mingw32-libxslt-use-correct-mkdir.patch -->
613 by Marcin Wojdyr
ccp4.xml: added more ccp4mg dependencies: suds, lxml, libxslt,
1516
  <autotools id="libxslt" autogenargs="--without-python --without-crypto --bindir=${prefix}/devbin">
1517
    <pkg-config>libxslt.pc</pkg-config>
1518
    <branch module="libxml2/libxslt-${version}.tar.gz"
1519
            repo="xmlsoft.org" version="1.1.28" size="3435907"/>
1520
    <dependencies>
1521
      <dep package="libxml2"/>
1522
    </dependencies>
1523
  </autotools>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1524
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1525
  <repository type="tarball" name="gc"
717 by Marcin Wojdyr
ccp4.xml: gc download location changed, update gc-alpha to gc-7.2e
1526
              href="http://www.hboehm.info/gc/gc_source/"/>
132 by Marcin Wojdyr
updated moduleset
1527
  <autotools id="gc" autogen-sh="configure"
718 by Marcin Wojdyr
ccp4.xml: gc configure needs --enable-cplusplus for rapper (how did it work
1528
             autogenargs="--disable-threads --enable-cplusplus">
717 by Marcin Wojdyr
ccp4.xml: gc download location changed, update gc-alpha to gc-7.2e
1529
    <branch module="gc-7.2e.tar.gz"
1530
            repo="gc" version="7.2e" checkoutdir="gc-7.2e" size="1291186"/>
110 by Marcin Wojdyr
updated moduleset
1531
  </autotools>
1532
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1533
  <repository type="tarball" name="lapack_site"
1534
              href="http://www.netlib.org/lapack/"/>
1047 by Marcin Wojdyr
always call cmake with -DBUILD_SHARED_LIBS=...
1535
  <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)
1536
    <branch repo="lapack_site" version="3.5.0" module="lapack-${version}.tgz"
1537
            size="6313139"/>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1538
  </cmake>
1539
232 by Marcin Wojdyr
disable parallel building (make -jN) of FFTW2, it sometimes goes wrong
1540
  <!-- compile in-source, otherwise fftw.h in srcdir is not modified by
1541
       configure; since the source could be already built by different
1542
       compiler we run make clean first (and -j1 to prevent clean and make
1543
       running in parallel -->
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1544
  <repository type="tarball" name="fftw_site" href="http://www.fftw.org/"/>
774 by Marcin Wojdyr
ccp4.xml: build fftw2 with fortran support
1545
  <autotools id="fftw2" autogenargs="--enable-float"
329 by Marcin Wojdyr
ccp4.xml: added guile-gtk, guile-gui, oldssm
1546
             supports-non-srcdir-builds="no" makeargs="-j1 clean all">
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1547
    <branch repo="fftw_site" module="fftw-2.1.5.tar.gz"
889 by Charles Ballard
workaround for quotes in GLOB_options for ifc
1548
            version="2.1.5" size="1256888">
1549
      <patch file="fftw2-configure.patch" strip="0" />
1550
    </branch>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1551
  </autotools>
1552
305 by Marcin Wojdyr
moduleset: added coot and a lot of dependencies
1553
  <repository type="tarball" name="jpeg" href="http://www.ijg.org/files/"/>
455 by Marcin Wojdyr
introduced directory devbin/ for binaries not needed after bulding is done
1554
  <autotools id="libjpeg" autogenargs="--bindir=${prefix}/devbin">
1095 by Marcin Wojdyr
update libjpeg and libtiff
1555
    <branch repo="jpeg" module="jpegsrc.v${version}.tar.gz" version="9a"
1556
            size="1000034" checkoutdir="jpeg-${version}"/>
82 by Marcin Wojdyr
moduleset: added libjpeg and reordered
1557
  </autotools>
1558
813 by Marcin Wojdyr
libpng: go back to autoconf & add patch to skip building programs
1559
  <autotools id="libpng" autogenargs="--bindir=${prefix}/devbin">
320 by Marcin Wojdyr
more coot dependencies
1560
    <pkg-config>libpng.pc</pkg-config>
306 by Marcin Wojdyr
added more coot dependencies
1561
    <branch repo="sf" module="libpng/libpng-${version}.tar.gz"
1094 by Marcin Wojdyr
update libpng 1.6.12 -> 1.6.18
1562
            version="1.6.18" size="1400221"/>
306 by Marcin Wojdyr
added more coot dependencies
1563
    <dependencies>
1564
      <dep package="zlib"/>
1565
    </dependencies>
813 by Marcin Wojdyr
libpng: go back to autoconf & add patch to skip building programs
1566
  </autotools>
306 by Marcin Wojdyr
added more coot dependencies
1567
1055 by Marcin Wojdyr
reverted freeglut to 2.8.1 -- too many build problems with 3.0.0
1568
  <autotools id="freeglut" autogenargs="">
1569
    <branch repo="sf" module="freeglut/freeglut-2.8.1.tar.gz"
1570
            version="2.8.1" size="1005343">
1571
      <patch file="freeglut-smooth_opengl3.patch" strip="0" />
1572
      <patch file="freeglut-strokechar.patch" strip="0" />
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
1573
    </branch>
339 by Marcin Wojdyr
added freeglut
1574
    <dependencies>
1575
    </dependencies>
1055 by Marcin Wojdyr
reverted freeglut to 2.8.1 -- too many build problems with 3.0.0
1576
  </autotools>
339 by Marcin Wojdyr
added freeglut
1577
372 by Marcin Wojdyr
ccp4.xml: add boost
1578
  <custom id="boost"
1245 by Charles Ballard
update RDKit to 2016_09_04
1579
          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
1580
          build="./b2 -q -d+2 -sNO_BZIP2=1 --layout=system variant=release link=shared linkflags=&quot;${LDFLAGS}&quot; stage"
1581
          install="./b2 -q -d+2 -sNO_BZIP2=1 --layout=system variant=release link=shared linkflags=&quot;${LDFLAGS}&quot; install --prefix=${dest}"
372 by Marcin Wojdyr
ccp4.xml: add boost
1582
          clean="./b2 --clean-all">
1182 by Marcin Wojdyr
downgrade boost to 1.59.0, because of:
1583
    <branch repo="sf" module="boost/boost/1.59.0/boost_1_59_0.tar.gz"
1584
            version="1.59.0" size="83709983">
1585
      <patch file="boost-make-setter.patch" strip="0" />
1586
    </branch>
393 by Marcin Wojdyr
ccp4.xml: boost depends on zlib and bzip2
1587
    <dependencies>
1588
      <dep package="zlib"/>
1589
    </dependencies>
372 by Marcin Wojdyr
ccp4.xml: add boost
1590
  </custom>
339 by Marcin Wojdyr
added freeglut
1591
1223 by Andrey Lebedev
changed url for libtiff
1592
  <repository type="tarball" name="tiff" href="http://download.osgeo.org/"/>
831 by Marcin Wojdyr
install libtiff and Pixie like other packages (libs in $CCP4/lib, etc)
1593
  <autotools id="tiff" autogenargs="--disable-lzma"
1594
             makeargs="SUBDIRS='port libtiff'"
1595
             makeinstallargs="SUBDIRS='port libtiff' install">
1095 by Marcin Wojdyr
update libjpeg and libtiff
1596
   <branch repo="tiff" module="libtiff/tiff-${version}.tar.gz"
1597
            version="4.0.5" size="2135410"/>
831 by Marcin Wojdyr
install libtiff and Pixie like other packages (libs in $CCP4/lib, etc)
1598
   <pkg-config>libtiff-4.pc</pkg-config>
1599
   <dependencies>
1600
     <dep package="zlib"/>
1601
     <dep package="libjpeg"/>
1602
   </dependencies>
1603
  </autotools>
765 by Ville Uski
Apply Stuart's patches to compile pixie with ccp4mg, and tiff with pixie.
1604
1143 by Marcin Wojdyr
added patch for pixie with all flex/bison generated files
1605
  <!-- 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)
1606
       they are regenerated after installation (triggers/pixie.trigger).
1607
       $PIXIEHOME is respected only on OSX, on Linux $SHADERS and $DISPLAY
1608
       need to be set.
765 by Ville Uski
Apply Stuart's patches to compile pixie with ccp4mg, and tiff with pixie.
1609
  -->
831 by Marcin Wojdyr
install libtiff and Pixie like other packages (libs in $CCP4/lib, etc)
1610
  <autotools id="pixie"
1611
             autogenargs="--bindir=${prefix}/libexec --disable-selfcontained"
1612
             supports-non-srcdir-builds="no">
1613
    <branch repo="sf" module="pixie/Pixie-src-2.2.6.tgz"
1614
            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.
1615
      <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
1616
      <patch file="pixie-generated.patch" strip="0"/>
831 by Marcin Wojdyr
install libtiff and Pixie like other packages (libs in $CCP4/lib, etc)
1617
    </branch>
765 by Ville Uski
Apply Stuart's patches to compile pixie with ccp4mg, and tiff with pixie.
1618
    <dependencies>
1619
      <dep package="tiff"/>
1620
    </dependencies>
831 by Marcin Wojdyr
install libtiff and Pixie like other packages (libs in $CCP4/lib, etc)
1621
  </autotools>
765 by Ville Uski
Apply Stuart's patches to compile pixie with ccp4mg, and tiff with pixie.
1622
390 by Marcin Wojdyr
ccp4.xml: tweak qt4 build
1623
  <!--
1624
  on Linux qt4 compilation requires dev files for fontconfig and xrender
1625
  -->
374 by Marcin Wojdyr
ccp4.xml: added qt4
1626
  <repository type="tarball" name="qt4"
1096 by Marcin Wojdyr
update Qt to 4.8.7
1627
              href="http://download.qt.io/official_releases/qt/"/>
502 by Marcin Wojdyr
reordered Qt4 configure arguments
1628
  <!-- the first lines (before -release) are unix-specific -->
374 by Marcin Wojdyr
ccp4.xml: added qt4
1629
  <custom id="qt4"
476 by Marcin Wojdyr
ccp4.xml: use "devbin" as bindir for qt4
1630
   configure="${srcdir}/configure -prefix ${prefix} -bindir ${prefix}/devbin
623 by Marcin Wojdyr
ccp4.xml: fix to the last commit (-plugindir)
1631
   -plugindir ${libdir}/qt4/plugins
502 by Marcin Wojdyr
reordered Qt4 configure arguments
1632
   -no-sse3 -no-ssse3 -no-sse4.1 -no-sse4.2 -no-avx
1633
   -fontconfig -opengl -no-sm -no-xshape -no-xvideo
374 by Marcin Wojdyr
ccp4.xml: added qt4
1634
   -release -opensource -xmlpatterns
729 by Marcin Wojdyr
qt4: remove -no-sse2 option from 64-bit build
1635
   -no-3dnow -no-neon
1189 by Marcin Wojdyr
do not disable sqlite support in qt4
1636
   -no-qt3support -qt-libmng
564 by Marcin Wojdyr
ccp4.xml: remove -no-dbus from qt4 options -- due to strange errors on some
1637
   -no-phonon -no-phonon-backend -no-multimedia
374 by Marcin Wojdyr
ccp4.xml: added qt4
1638
   -no-audio-backend -webkit -no-declarative -no-declarative-debug
603 by Charles Ballard
QtWebkit fails to compile on OS X if QScript is not there, so remove -no-script
1639
   -no-scripttools
564 by Marcin Wojdyr
ccp4.xml: remove -no-dbus from qt4 options -- due to strange errors on some
1640
   -no-cups -no-openvg
374 by Marcin Wojdyr
ccp4.xml: added qt4
1641
   -no-s60 -nomake examples -nomake demos -nomake tools -confirm-license"
390 by Marcin Wojdyr
ccp4.xml: tweak qt4 build
1642
   build="${}" install="make INSTALL_ROOT=${destdir} install" clean="${}"
374 by Marcin Wojdyr
ccp4.xml: added qt4
1643
   supports-non-srcdir-builds="yes">
1096 by Marcin Wojdyr
update Qt to 4.8.7
1644
    <branch repo="qt4" version="4.8.7" size="241075567"
1645
            module="4.8/4.8.7/qt-everywhere-opensource-src-4.8.7.tar.gz"/>
374 by Marcin Wojdyr
ccp4.xml: added qt4
1646
    <dependencies>
1647
      <dep package="zlib"/>
1648
      <dep package="libpng"/>
1649
      <dep package="libjpeg"/>
1650
      <dep package="openssl"/>
859 by Marcin Wojdyr
ccp4.xml: build qt4 with mng and tiff support (requested for i2)
1651
      <dep package="tiff"/>
1189 by Marcin Wojdyr
do not disable sqlite support in qt4
1652
      <dep package="sqlite3"/>
374 by Marcin Wojdyr
ccp4.xml: added qt4
1653
    </dependencies>
980 by Marcin Wojdyr
ccp4.xml: note that qt4 may depend on glib (on Linux)
1654
    <after> <!-- on Linux it may use glib -->
1655
      <dep package="glib"/>
1656
    </after>
374 by Marcin Wojdyr
ccp4.xml: added qt4
1657
  </custom>
1658
1292 by Tom Burnley
add qt5 to ccpem
1659
  <repository type="tarball" name="qt5"
1660
              href="http://download.qt.io/official_releases/qt/"/>
1661
  <!-- the first lines (before -release) are unix-specific -->
1662
  <custom id="qt5"
1663
   configure="${srcdir}/configure -prefix ${prefix} -bindir ${prefix}/devbin
1664
   -plugindir ${libdir}/qt5/plugins
1665
   -no-sse3 -no-ssse3 -no-sse4.1 -no-sse4.2 -no-avx
1666
   -fontconfig -opengl -no-sm -no-xshape -no-xvideo
1667
   -release -opensource -xmlpatterns
1668
   -no-3dnow -no-neon
1669
   -no-qt3support -qt-libmng
1670
   -no-phonon -no-phonon-backend -no-multimedia
1671
   -no-audio-backend -webkit -no-declarative -no-declarative-debug
1672
   -no-scripttools
1673
   -no-cups -no-openvg
1674
   -no-s60 -nomake examples -nomake demos -nomake tools -confirm-license"
1675
   build="${}" install="make INSTALL_ROOT=${destdir} install" clean="${}"
1676
   supports-non-srcdir-builds="yes">
1677
    <branch repo="qt5" version="5.9.2"
1678
            module="5.9/5.9.2/single/qt-everywhere-opensource-src-5.9.2.tar.xz"/>
1679
    <dependencies>
1680
      <dep package="zlib"/>
1681
      <dep package="libpng"/>
1682
      <dep package="libjpeg"/>
1683
      <dep package="openssl"/>
1684
      <dep package="tiff"/>
1685
      <dep package="sqlite3"/>
1686
    </dependencies>
1687
    <after> <!-- on Linux it may use glib XXX check if required for qt5?-->
1688
      <dep package="glib"/>
1689
    </after>
1690
  </custom>
1691
976 by Marcin Wojdyr
ccp4.xml: pass LDFLAGS also to pyqt4
1692
  <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
1693
          build="${}" install="${}" clean="${}"
1694
          supports-non-srcdir-builds="no">
1695
    <branch repo="sf" module="pyqt/sip/sip-${version}/sip-${version}.tar.gz"
1101 by Marcin Wojdyr
update sip and pyqt4
1696
            version="4.16.9" size="957858"/>
617 by Marcin Wojdyr
ccp4.xml: sip: change dependency on Python to "after" Python (building
1697
    <after>
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1698
      <dep package="python"/>
617 by Marcin Wojdyr
ccp4.xml: sip: change dependency on Python to "after" Python (building
1699
    </after>
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1700
  </custom>
1701
1702
  <custom id="pyqt4"
1266 by Tom Burnley
add dssp dep to ccpem
1703
          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;${LDFLAGS}&quot;"
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1704
          build="${}" install="${} INSTALL_ROOT=${destdir}" clean="${}"
1705
          supports-non-srcdir-builds="yes">
622 by Marcin Wojdyr
ccp4.xml: build qt4 with -plugindir ${libdir}/qt4
1706
    <!-- no real differences between PyQt-mac and PyQt-x11, only differences
1707
         in doc/html/ and in comments in sip/ -->
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1708
    <branch repo="sf"
1709
            module="pyqt/PyQt4/PyQt-${version}/PyQt-x11-gpl-${version}.tar.gz"
1101 by Marcin Wojdyr
update sip and pyqt4
1710
            version="4.11.4" size="11317088"/>
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1711
    <dependencies>
1712
      <dep package="sip"/>
735 by Marcin Wojdyr
ccp4.xml: pyqt4 4.10.3 -> 4.10.4 (should fix some build problems)
1713
    </dependencies>
1714
    <after>
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1715
      <dep package="qt4"/>
735 by Marcin Wojdyr
ccp4.xml: pyqt4 4.10.3 -> 4.10.4 (should fix some build problems)
1716
    </after>
395 by Marcin Wojdyr
ccp4.xml: added sip and qt4
1717
  </custom>
1718
613 by Marcin Wojdyr
ccp4.xml: added more ccp4mg dependencies: suds, lxml, libxslt,
1719
  <distutils id="suds">
1720
    <branch repo="pypi" module="s/suds/suds-${version}.tar.gz"
1721
            version="0.4" size="104013"/>
1722
    <dependencies/>
1723
    <after>
1724
      <dep package="python"/>
1725
      <dep package="setuptools"/>
1726
    </after>
1727
  </distutils>
1728
1729
  <distutils id="lxml">
1294 by Tom Burnley
update lxml to version 4.1.0; hopefully removes liblzma error
1730
    <branch repo="pypi" module="../89/dc/ec07a5adf6afb02ad4f5f7e1f7e1a2fc0e3d88ce4fe233ed4b3dabd07cbd/lxml-${version}.tar.gz"
1731
            version="4.1.0"/>
613 by Marcin Wojdyr
ccp4.xml: added more ccp4mg dependencies: suds, lxml, libxslt,
1732
    <dependencies>
1733
      <dep package="libxml2"/>
1734
      <dep package="libxslt"/>
1735
    </dependencies>
1736
    <after>
1737
      <dep package="python"/>
1738
      <dep package="setuptools"/>
1739
    </after>
1740
  </distutils>
1741
349 by Marcin Wojdyr
added raster3d-cmake.patch
1742
  <repository type="tarball" name="raster3d"
1743
              href="http://skuld.bmsc.washington.edu/raster3d/"/>
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
1744
  <cmake id="raster3d">
949 by Marcin Wojdyr
updated raster3d
1745
    <branch repo="raster3d" module="Raster3D_${version}.tar.gz" version="3.0-3">
1148 by Marcin Wojdyr
Raster3d CMakeLists.txt: +include_directories(${GD_INCLUDE_DIR})
1746
      <patch file="raster3d-cmake.patch" strip="0" />
349 by Marcin Wojdyr
added raster3d-cmake.patch
1747
    </branch>
307 by Marcin Wojdyr
ccp4.xml: added raster3d and libgd
1748
    <dependencies>
1749
      <dep package="libgd"/>
1750
    </dependencies>
1751
  </cmake>
1752
588 by Marcin Wojdyr
ccp4.xml: added plplot
1753
  <cmake id="plplot" cmakeargs="-DENABLE_DYNDRIVERS=0 -DDEFAULT_NO_BINDINGS=1 -DHAVE_QHULL=0 -DWITH_CSA=0 -DDEFAULT_NO_DEVICES=1 -DPLD_png=1">
1754
    <branch repo="sf"
1755
            module="plplot/plplot/${version}%20Source/plplot-${version}.tar.gz"
1054 by Marcin Wojdyr
update plplot to 5.11.0 (because of building problems on OSX Yosemite)
1756
            version="5.11.0" size="15892751">
773 by Marcin Wojdyr
ccp4.xml: use $CCP4 instead of $PLPLOT_HOME in plplot
1757
      <patch file="plplot-home-env.patch" strip="0" />
1758
    </branch>
588 by Marcin Wojdyr
ccp4.xml: added plplot
1759
    <dependencies>
1760
      <dep package="libgd"/>
1761
    </dependencies>
1762
  </cmake>
1763
966 by Marcin Wojdyr
add macapp
1764
  <cmake id="macapp">
1765
    <branch/>
1766
  </cmake>
1767
951 by Marcin Wojdyr
add special hack for ccpforge anonymous svn to jhbuild/versioncontrol/svn.py
1768
  <!-- ccpforge is handled by special hack in jhbuild/versioncontrol/svn.py -->
840 by Marcin Wojdyr
ccp4.xml: added ccpem
1769
  <repository type="svn" name="ccpforge"
1201 by Marcin Wojdyr
ccpem repo url changed to https
1770
              href="https://anonymous@ccpforge.cse.rl.ac.uk/svn/"/>
840 by Marcin Wojdyr
ccp4.xml: added ccpem
1771
  <cmake id="ccpem">
1772
    <branch repo="ccpforge" module="ccpem/"/>
1773
    <dependencies>
1293 by Tom Burnley
revert ccpem deps for standard qt4 build
1774
<!--      <dep package="qt5"/>-->
1277 by Tom Burnley
update to include modeller dep for ccpem
1775
      <dep package="modeller"/>
1204 by Marcin Wojdyr
more dependencies for ccpem
1776
      <dep package="ccp4-base"/>
1777
      <dep package="libccp4"/>
1220 by Tom Burnley
add ccp4 lib data as ccpem dep
1778
      <dep package="ccp4-lib-data"/>
866 by Marcin Wojdyr
ccpem dependency changed from mmdb to mmdb2
1779
      <dep package="mmdb2"/>
840 by Marcin Wojdyr
ccp4.xml: added ccpem
1780
      <dep package="clipper"/>
1219 by Tom Burnley
add clipper_progs to ccp4.xml
1781
      <dep package="clipper-progs"/>
1140 by Marcin Wojdyr
ccpem: added deps python, qtrview, jsrview as requested by Tom
1782
      <dep package="python"/>
1156 by Marcin Wojdyr
ccpem module changes for Tom
1783
      <dep package="numpy"/>
1198 by Marcin Wojdyr
more dependencies for ccpem
1784
      <dep package="scipy"/>
1200 by Marcin Wojdyr
ccpem requires pandas
1785
      <dep package="pandas"/>
1198 by Marcin Wojdyr
more dependencies for ccpem
1786
      <dep package="pillow"/>
1272 by Tom Burnley
update version of pytest and xdist
1787
      <dep package="pytest"/>
1207 by Marcin Wojdyr
add pytest and pytest-xdist for ccpem
1788
      <dep package="pytest-xdist"/>
1198 by Marcin Wojdyr
more dependencies for ccpem
1789
      <dep package="biopython"/>
1790
      <dep package="matplotlib"/>
1791
      <dep package="clipper-python"/>
1140 by Marcin Wojdyr
ccpem: added deps python, qtrview, jsrview as requested by Tom
1792
      <dep package="jsrview"/>
1204 by Marcin Wojdyr
more dependencies for ccpem
1793
      <dep package="molrep"/>
1281 by Tom Burnley
add refmac back into ccpem; disable coot for testing on osx build
1794
      <dep package="refmac"/>
1204 by Marcin Wojdyr
more dependencies for ccpem
1795
      <dep package="sfcheck"/>
1210 by Tom Burnley
Add more deps for ccp-em
1796
      <dep package="monomers"/>
1797
      <dep package="ccp4-progs"/>
1229 by Marcin Wojdyr
the contact prediction interface was renamed from CPTBX to ConKit
1798
      <dep package="conkit"/>
1283 by ronan.keegan at ac
Added build options for pyjob and simbad
1799
      <dep package="pyjob"/>
1800
      <dep package="simbad"/>
1234 by Marcin Wojdyr
add mrcfile for ccpem
1801
      <dep package="mrcfile"/>
1289 by Tom Burnley
add mpi4py, return coot to ccpem
1802
      <dep package="coot"/>
1276 by Tom Burnley
add prosmart back as ccpem dep
1803
      <dep package="prosmart"/>
1267 by Tom Burnley
add xssp dep for ccpem
1804
      <dep package="xssp"/>
1290 by Tom Burnley
remove ccp-em loc-scale dep for now
1805
<!--      <dep package="loc-scale"/>-->
1291 by Tom Burnley
remove mpi4py for now
1806
<!--      <dep package="mpi4py"/>-->
840 by Marcin Wojdyr
ccp4.xml: added ccpem
1807
    </dependencies>
1808
  </cmake>
1809
1234 by Marcin Wojdyr
add mrcfile for ccpem
1810
  <distutils id="mrcfile">
1811
    <branch repo="github" module="ccpem/mrcfile.git"/>
1812
    <dependencies>
1813
      <dep package="numpy"/>
1814
    </dependencies>
1815
  </distutils>
1816
1289 by Tom Burnley
add mpi4py, return coot to ccpem
1817
1818
<!--  <repository type="tarball" name="git-lab" href="https://git.embl.de"/>-->
1819
<!--  <distutils id="loc-scale">-->
1820
<!--    <branch repo="git-lab" module="jakobi/LocScale/raw/master/download/locscale.tgz"-->
1821
<!--            version="0.1"/>-->
1822
<!--    <after>-->
1823
<!--      <dep package="python"/>-->
1824
<!--      <dep package="numpy"/>-->
1825
<!--    </after>-->
1826
<!--  </distutils>-->
1827
1828
1829
<!--  <repository type="git" name="git-lab" href="https://git.embl.de"/>-->
1830
<!--  <distutils id="loc-scale">-->
1831
<!--    <branch repo="git-lab" module="jakobi/LocScale"/>-->
1832
<!--    <dependencies>-->
1833
<!--      <dep package="numpy"/>-->
1834
<!--    </dependencies>-->
1835
<!--  </distutils>-->
1836
1243 by Charles Ballard
control conkit installation
1837
  <distutils id="conkit"
1838
    buildargs="--script-python-path ccp4-python"
1839
    installargs="--install-scripts ${prefix}/bin --install-lib ${prefix}/lib/py2/site-packages ">
1230 by ronan.keegan at ac
Updated conkit build with versioning
1840
      <branch repo="github-zip"
1284 by ronan.keegan at ac
update ccp4.xml for ample/simbad
1841
          version="0.8.3"
1239 by Tom Burnley
move to ConKit to ridgenlab github account
1842
          module="rigdenlab/conkit/archive/${version}.zip"
1240 by Charles Ballard
patch bin/python in conkit to ccp4-python
1843
          checkoutdir="conkit-${version}">
1844
      </branch>
1227 by Marcin Wojdyr
add cptbx for ccpem
1845
    <dependencies>
1846
      <dep package="numpy"/>
1847
      <dep package="biopython"/>
1230 by ronan.keegan at ac
Updated conkit build with versioning
1848
      <dep package="matplotlib"/>
1849
      <dep package="scipy"/>
1227 by Marcin Wojdyr
add cptbx for ccpem
1850
    </dependencies>
1851
    <after>
1852
      <dep package="python"/>
1853
      <dep package="setuptools"/>
1854
    </after>
1855
  </distutils>
1856
1283 by ronan.keegan at ac
Added build options for pyjob and simbad
1857
  <distutils id="pyjob"
1858
    installargs="--install-scripts ${prefix}/bin --install-lib ${prefix}/lib/py2/site-packages ">
1859
      <branch repo="github-zip"
1860
          version="0.1.3"
1861
          module="fsimkovic/pyjob/archive/${version}.zip"
1862
          checkoutdir="pyjob-${version}">
1863
      </branch>
1864
    <dependencies>
1865
      <dep package="numpy"/>
1866
    </dependencies>
1867
    <after>
1868
      <dep package="python"/>
1869
      <dep package="setuptools"/>
1870
    </after>
1871
  </distutils>
1872
1284 by ronan.keegan at ac
update ccp4.xml for ample/simbad
1873
  <cmake id="simbad">
1874
    <branch repo="github-zip"
1287 by ronan.keegan at ac
Update to version 0.0.6 of SIMBAD
1875
            version="0.0.6"
1284 by ronan.keegan at ac
update ccp4.xml for ample/simbad
1876
            module="rigdenlab/simbad/archive/${version}.zip"
1877
            checkoutdir="simbad-${version}">
1878
    </branch>
1283 by ronan.keegan at ac
Added build options for pyjob and simbad
1879
    <dependencies>
1880
      <dep package="numpy"/>
1881
      <dep package="pandas"/>
1882
      <dep package="pyjob"/>
1883
    </dependencies>
1284 by ronan.keegan at ac
update ccp4.xml for ample/simbad
1884
  </cmake>
1283 by ronan.keegan at ac
Added build options for pyjob and simbad
1885
1049 by Marcin Wojdyr
ccp4.xml: add longbow for ccpem
1886
  <repository type="git" name="bitbucket-git" href="https://bitbucket.org/"/>
1887
  <distutils id="longbow">
1888
    <branch repo="bitbucket-git" module="jimboid/longbow.git"/>
1889
    <after>
1890
      <dep package="python"/>
1891
    </after>
1892
  </distutils>
1893
1076 by Marcin Wojdyr
added probe and reduce from github.com/rlabduke
1894
  <cmake id="probe">
1895
    <branch repo="github-zip"
1896
        module="rlabduke/probe/archive/${version}.zip"
1897
        version="acc7f517c3e3830b2489f71cbc53049399f86909"
1898
        checkoutdir="probe-${version}">
1899
      <patch file="probe-cmake.patch" strip="0" />
1900
    </branch>
1901
  </cmake>
1902
1903
  <cmake id="reduce">
1904
    <branch repo="github-zip"
1905
        module="rlabduke/reduce/archive/${version}.zip"
1906
        version="9fb41bbc04a2b611832231fcfc7ab8f670083bef"
1907
        checkoutdir="reduce-${version}">
1908
      <patch file="reduce-cmake.patch" strip="0" />
1909
    </branch>
1910
  </cmake>
1911
1139 by Andrey Lebedev
arcimboldo is now build from sources; added ecdsa module
1912
<!--
1121 by Marcin Wojdyr
add arcimboldo
1913
  <custom id="arcimboldo" install_to="bin/* bin/, arcimboldo lib/py2/">
1914
    <branch repo="files" version="3.0.1-test1"
1915
            module="arcimboldo-${version}.tar.gz"/>
1139 by Andrey Lebedev
arcimboldo is now build from sources; added ecdsa module
1916
-->
1917
  <cmake id="arcimboldo">
1918
    <branch/>
1121 by Marcin Wojdyr
add arcimboldo
1919
    <dependencies>
1920
      <dep package="scipy"/>
1921
      <dep package="biopython"/>
1922
      <dep package="matplotlib"/>
1923
      <dep package="paramiko"/>
1139 by Andrey Lebedev
arcimboldo is now build from sources; added ecdsa module
1924
      <dep package="ecdsa"/>
1121 by Marcin Wojdyr
add arcimboldo
1925
    </dependencies>
1139 by Andrey Lebedev
arcimboldo is now build from sources; added ecdsa module
1926
  </cmake>
1121 by Marcin Wojdyr
add arcimboldo
1927
1282 by Andrey Lebedev
added morda-mp
1928
  <cmake id="morda-mp">
1929
    <branch/>
1930
    <dependencies/>
1931
  </cmake>
1932
1225 by Marcin Wojdyr
add panddas (Unix-only for now)
1933
  <distutils id="panddas" buildargs="--for-ccp4">
1271 by Charles Ballard
udpate panddas to 0.2.5
1934
    <branch repo="pypi" version="0.2.5" size="4197609"
1935
            module="../9c/8c/03640979aef7e457673acdb447ac7bef102d222e16429d39423105f54da7/panddas-${version}.tar.gz"/>
1175 by Marcin Wojdyr
add pandas
1936
    <dependencies>
1937
      <dep package="pandas"/>
1938
      <dep package="scipy"/>
1199 by Marcin Wojdyr
add MarkupSafe for PANDDA
1939
      <dep package="markupsafe"/>
1175 by Marcin Wojdyr
add pandas
1940
      <dep package="jinja2"/>
1941
    </dependencies>
1225 by Marcin Wojdyr
add panddas (Unix-only for now)
1942
  </distutils>
1175 by Marcin Wojdyr
add pandas
1943
1142 by Andrey Lebedev
added lorestr
1944
  <cmake id="lorestr">
1945
    <branch/>
1946
    <dependencies />
1947
  </cmake>
1948
1251 by Andrey Lebedev
added pdb deposition
1949
  <cmake id="pdbdeposition">
1950
    <branch/>
1951
    <dependencies />
1952
  </cmake>
1953
49 by Marcin Wojdyr
added shared/static static options to autogenargs,
1954
  <metamodule id="default">
1 by Marcin Wojdyr
initial revision of jhbuild config
1955
    <dependencies>
957 by Marcin Wojdyr
updates for ccp4-core -> ccp4-base, ... transition
1956
      <dep package="ccp4-base"/>
1957
      <dep package="ccp4-lib-data"/>
881 by Marcin Wojdyr
ccp4.xml: use mmdb2 everywhere
1958
      <dep package="mmdb2"/>
1 by Marcin Wojdyr
initial revision of jhbuild config
1959
      <dep package="ccif"/>
177 by Marcin Wojdyr
updated moduleset
1960
      <dep package="libccp4"/>
1 by Marcin Wojdyr
initial revision of jhbuild config
1961
      <dep package="ssm"/>
1962
      <dep package="ccp4srs"/>
47 by Marcin Wojdyr
updated modules list (not tested)
1963
      <dep package="gesamt"/>
177 by Marcin Wojdyr
updated moduleset
1964
      <dep package="molrep"/>
219 by Marcin Wojdyr
updated moduleset to add new bzr modules
1965
      <dep package="sfcheck"/>
1966
      <dep package="procheck"/>
1967
      <dep package="scala"/>
1968
      <dep package="dm21"/>
7 by Marcin Wojdyr
added refmac
1969
      <dep package="refmac"/>
190 by Marcin Wojdyr
moduleset changes: new LAPACK, refmac_dictionary is now in bazaar
1970
      <dep package="monomers"/>
15 by Marcin Wojdyr
added ccp4 from CVS (with cmake) to ccp4.modules
1971
      <dep package="ccp4-progs"/>
31 by Marcin Wojdyr
ccp4-jhbuild: added ccp4i to ccp4-all
1972
      <dep package="ccp4i"/>
219 by Marcin Wojdyr
updated moduleset to add new bzr modules
1973
      <dep package="imosflm"/>
35 by Marcin Wojdyr
added clipper to ccp4.modules, now trying to add cctbx...
1974
      <dep package="clipper"/>
1975
      <dep package="pointless"/>
1976
      <dep package="aimless"/>
670 by Charles Ballard
trunk gets feckless build
1977
      <dep package="feckless"/>
56 by Marcin Wojdyr
a few small updates
1978
      <dep package="clipper-progs"/>
192 by Marcin Wojdyr
cprodrg is now in bzr, CVS no longer needed
1979
      <dep package="cprodrg"/>
79 by Marcin Wojdyr
ccp4.xml: added prosmart and updated ccp4-progs
1980
      <dep package="prosmart"/>
686 by Marcin Wojdyr
ccp4.xml: added crank2
1981
      <dep package="crank2"/>
177 by Marcin Wojdyr
updated moduleset
1982
      <dep package="examples"/>
1983
      <dep package="documentation"/>
365 by Marcin Wojdyr
minor tweaks
1984
      <dep package="ccp4dispatchers"/>
279 by Marcin Wojdyr
moduleset: added edstats
1985
      <dep package="edstats"/>
284 by Marcin Wojdyr
moduleset: added dimple to default set of packages
1986
      <dep package="dimple"/>
316 by Marcin Wojdyr
ccp4.xml: added tgutils to "all"
1987
      <dep package="mrbump"/>
1988
      <dep package="tgutils"/>
647 by ronan.keegan at ac
added spicker build
1989
      <dep package="spicker"/>
744 by ronan.keegan at ac
added prelyscar to 'all' option
1990
      <dep package="prelyscar"/>
652 by ronan.keegan at ac
Added theseus 2.0.6 to the build
1991
      <dep package="theseus"/>
177 by Marcin Wojdyr
updated moduleset
1992
      <!-- may depend on Tcl -->
101 by Marcin Wojdyr
updated ccp4-jhbuild
1993
      <dep package="diff-image"/>
122 by Marcin Wojdyr
added ccp4mapwish module
1994
      <dep package="ccp4mapwish"/>
188 by Marcin Wojdyr
jligand is now in bazaar
1995
      <!-- requires javac -->
1996
      <dep package="jligand"/>
177 by Marcin Wojdyr
updated moduleset
1997
      <!-- pulls libxml, gc -->
47 by Marcin Wojdyr
updated modules list (not tested)
1998
      <dep package="rapper"/>
177 by Marcin Wojdyr
updated moduleset
1999
      <!-- requires Qt, OpenGL -->
223 by Marcin Wojdyr
ccp4.xml updated to reflect recent changes in qt-using programs
2000
      <dep package="pisa"/>
177 by Marcin Wojdyr
updated moduleset
2001
      <dep package="viewhkl"/>
220 by Marcin Wojdyr
added qtrview
2002
      <dep package="qtrview"/>
242 by Marcin Wojdyr
updated README and ccp4.xml
2003
      <!-- for now Ample is tested/working only on Unix -->
2004
      <dep package="ample"/>
365 by Marcin Wojdyr
minor tweaks
2005
      <dep package="raster3d"/>
1119 by Marcin Wojdyr
ccp4.xml: replace dssp with xssp in "default"
2006
      <dep package="xssp"/>
627 by Marcin Wojdyr
ccp4.xml: add blend
2007
      <dep package="blend"/>
827 by Marcin Wojdyr
ccp4.xml: add acedrg to "all"
2008
      <dep package="acedrg"/>
906 by Marcin Wojdyr
ccp4.xml: add libg
2009
      <dep package="libg"/>
875 by Marcin Wojdyr
ccp4.xml: add privateer to "all"
2010
      <dep package="privateer"/>
915 by Marcin Wojdyr
ccp4.xml: move biosequence tools from "ccp4-linux" to "default"
2011
      <dep package="clustalw2"/>
2012
      <dep package="mafft"/>
2013
      <dep package="hmmer"/>
1023 by Marcin Wojdyr
modified dependecies: added ccp4mg to "default", pixie and matplotlib to ccp4mg,
2014
      <dep package="ccp4mg"/>
1012 by Marcin Wojdyr
add biopython to "all", for ccp4i2
2015
      <dep package="biopython"/>
1023 by Marcin Wojdyr
modified dependecies: added ccp4mg to "default", pixie and matplotlib to ccp4mg,
2016
      <dep package="jsrview"/>
1065 by Marcin Wojdyr
add clipper-python and ccp4srs-python to the build
2017
      <dep package="clipper-python"/>
2018
      <dep package="ccp4srs-python"/>
1116 by Marcin Wojdyr
ccp4.xml: don't include i2 in the default set for now, due to its size
2019
      <!-- dep package="ccp4i2"/-->
1077 by Marcin Wojdyr
ccp4.xml: add probe and reduce to "default"
2020
      <dep package="probe"/>
2021
      <dep package="reduce"/>
1251 by Andrey Lebedev
added pdb deposition
2022
      <dep package="pdbdeposition"/>
55 by Marcin Wojdyr
fixed module syntax
2023
    </dependencies>
1 by Marcin Wojdyr
initial revision of jhbuild config
2024
  </metamodule>
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
2025
445 by Marcin Wojdyr
replaced ccp4-unix with ccp4-osx and ccp4-linux
2026
  <metamodule id="ccp4-linux"> <!-- for Linux binaries  -->
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
2027
    <dependencies>
914 by Marcin Wojdyr
ccp4.xml: removed metamodule "all" (too many metamodules)
2028
      <dep package="default"/>
687 by Marcin Wojdyr
ccp4.xml: build tcltk84 on Linux by default
2029
      <dep package="tcltk84"/>
277 by Marcin Wojdyr
added hklview and a few other modules
2030
      <dep package="hklview"/>
399 by Marcin Wojdyr
added mosflm
2031
      <dep package="rotgen"/>
2032
      <dep package="mosflm"/>
925 by Marcin Wojdyr
ccp4.xml: build chooch on Unix
2033
      <dep package="chooch"/>
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
2034
      <dep package="pdb-extract"/>
1121 by Marcin Wojdyr
add arcimboldo
2035
      <dep package="arcimboldo"/>
1282 by Andrey Lebedev
added morda-mp
2036
      <dep package="morda-mp"/>
1142 by Andrey Lebedev
added lorestr
2037
      <dep package="lorestr"/>
1225 by Marcin Wojdyr
add panddas (Unix-only for now)
2038
      <dep package="panddas"/>
207 by Marcin Wojdyr
moduleset: build pdb-extract from our repository
2039
    </dependencies>
2040
  </metamodule>
370 by Marcin Wojdyr
added all-sources metamodule to ccp4.xml and updated README
2041
445 by Marcin Wojdyr
replaced ccp4-unix with ccp4-osx and ccp4-linux
2042
  <metamodule id="ccp4-osx"> <!-- for OSX binaries  -->
2043
    <dependencies>
2044
      <dep package="pkgconf"/>
2045
      <dep package="freetype2"/>
1041 by Marcin Wojdyr
bootstrap patchelf on Linux
2046
      <dep package="default"/>
2047
      <dep package="tcltk84"/>
2048
      <dep package="hklview"/>
2049
      <dep package="rotgen"/>
2050
      <dep package="mosflm"/>
2051
      <dep package="chooch"/>
2052
      <dep package="pdb-extract"/>
1121 by Marcin Wojdyr
add arcimboldo
2053
      <dep package="arcimboldo"/>
1282 by Andrey Lebedev
added morda-mp
2054
      <dep package="morda-mp"/>
1142 by Andrey Lebedev
added lorestr
2055
      <dep package="lorestr"/>
1225 by Marcin Wojdyr
add panddas (Unix-only for now)
2056
      <dep package="panddas"/>
445 by Marcin Wojdyr
replaced ccp4-unix with ccp4-osx and ccp4-linux
2057
    </dependencies>
2058
  </metamodule>
2059
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
2060
  <metamodule id="coot-osx"> <!-- extra for coot on os x -->
2061
    <dependencies>
2062
      <dep package="pkgconf"/>
2063
      <dep package="freetype2"/>
843 by Charles Ballard
add coot8-osx target and bring coot-osx more uptodate
2064
      <dep package="intltool"/>
2065
      <!--<dep package="gettext"/>-->
2066
      <!--<dep package="fontconfig"/>-->
2067
      <!--<dep package="readline"/>-->
768 by Charles Ballard
add coot-osx for older macs, including adding gettext, fontconfig and readline
2068
      <dep package="coot"/>
2069
    </dependencies>
843 by Charles Ballard
add coot8-osx target and bring coot-osx more uptodate
2070
    <after>
2071
      <dep package="python"/>
2072
    </after>
2073
  </metamodule>
2074
445 by Marcin Wojdyr
replaced ccp4-unix with ccp4-osx and ccp4-linux
2075
  <metamodule id="ccp4-windows"> <!-- for Windows -->
371 by Marcin Wojdyr
changes for source bundles
2076
    <dependencies>
403 by Marcin Wojdyr
ccp4.xml: add pkgconf to ccp4-windows
2077
      <dep package="pkgconf"/>
495 by Marcin Wojdyr
ccp4.xml: build libgnurx by default on Windows
2078
      <dep package="libgnurx"/>
371 by Marcin Wojdyr
changes for source bundles
2079
      <dep package="freetype2"/>
914 by Marcin Wojdyr
ccp4.xml: removed metamodule "all" (too many metamodules)
2080
      <dep package="default"/>
371 by Marcin Wojdyr
changes for source bundles
2081
    </dependencies>
2082
  </metamodule>
2083
969 by Marcin Wojdyr
ccp4.xml: added balbesdb and metamodule balbes
2084
  <metamodule id="balbes">
2085
    <dependencies>
2086
      <dep package="balbes-pipeline"/>
2087
      <dep package="balbesdb"/>
2088
    </dependencies>
2089
  </metamodule>
2090
370 by Marcin Wojdyr
added all-sources metamodule to ccp4.xml and updated README
2091
  <metamodule id="all-sources"> <!-- sources for ccp4 source bundle -->
2092
    <dependencies>
445 by Marcin Wojdyr
replaced ccp4-unix with ccp4-osx and ccp4-linux
2093
      <dep package="ccp4-linux"/>
674 by Marcin Wojdyr
ccp4.xml: add dssp to all, libgnurx to all-sources
2094
      <dep package="ccp4-windows"/>
2095
      <dep package="ccp4-osx"/>
370 by Marcin Wojdyr
added all-sources metamodule to ccp4.xml and updated README
2096
      <dep package="ccp4-deprecated"/>
2097
      <!-- <dep package="setup"/> -->
2098
      <dep package="devtools"/>
2099
      <dep package="python"/>
2100
      <dep package="setuptools"/>
2101
      <dep package="pip"/>
2102
      <dep package="bzr"/>
2103
      <dep package="cmake"/>
1023 by Marcin Wojdyr
modified dependecies: added ccp4mg to "default", pixie and matplotlib to ccp4mg,
2104
      <dep package="coot"/>
1133 by Marcin Wojdyr
ccp4.xml: add patchelf to all-sources
2105
      <dep package="patchelf"/>
370 by Marcin Wojdyr
added all-sources metamodule to ccp4.xml and updated README
2106
    </dependencies>
2107
  </metamodule>
371 by Marcin Wojdyr
changes for source bundles
2108
1 by Marcin Wojdyr
initial revision of jhbuild config
2109
</moduleset>
6 by Marcin Wojdyr
added pisa
2110
<!-- vim:set ts=2 sw=2 expandtab: -->