1 |
commit: aba20d3142c80878bbc1a3b045f14c849a63cb63 |
2 |
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in> |
3 |
AuthorDate: Sat May 29 13:37:10 2021 +0000 |
4 |
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> |
5 |
CommitDate: Sat May 29 15:48:30 2021 +0000 |
6 |
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=aba20d31 |
7 |
|
8 |
sci-biology/cmdock: add 0.1.3 |
9 |
|
10 |
* revise deps |
11 |
* fix symlinks |
12 |
* replace slotting with subslotting |
13 |
|
14 |
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in> |
15 |
|
16 |
sci-biology/cmdock/Manifest | 1 + |
17 |
sci-biology/cmdock/cmdock-0.1.2.ebuild | 29 +++---- |
18 |
.../{cmdock-0.1.2.ebuild => cmdock-0.1.3.ebuild} | 35 ++++---- |
19 |
.../files/{app_info.xml => app_info_0.1.2.xml} | 2 +- |
20 |
sci-biology/cmdock/files/app_info_0.1.3.xml | 95 ++++++++++++++++++++++ |
21 |
.../cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml | 15 ++++ |
22 |
.../cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 3 +- |
23 |
.../cmdock/files/cmdock-boinc_job_0.1.3.xml | 10 +++ |
24 |
8 files changed, 155 insertions(+), 35 deletions(-) |
25 |
|
26 |
diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest |
27 |
index 25663d438..c20f5e305 100644 |
28 |
--- a/sci-biology/cmdock/Manifest |
29 |
+++ b/sci-biology/cmdock/Manifest |
30 |
@@ -1 +1,2 @@ |
31 |
DIST cmdock-v0.1.2.tar.gz 13394195 BLAKE2B bd377b6a953d1e38b527da4eda36aee7a634e9f0c400487d4092ae1939589890038fc90052d8bddb25457dd027fa929acd50e836d65bd5994af89116f4c770a7 SHA512 90d4114a10dde99d34cd7ea4b28399da744cc295adebb10f1f9771b59841cd13e07cae5218643c90dd2847cdb014867ab795649a3d1883396a3609c3344b8226 |
32 |
+DIST cmdock-v0.1.3.tar.gz 13416412 BLAKE2B abd6382943fb2ca2459fa493f8025e335821b96a95b88267dd493c28cd3280481b41ec6480fd3514cff126ab1077e89f075e5311393b1cd366403419e9c47454 SHA512 d941b672d14bad4fda4eaeb7aa313da1ade213241a1aee392747943a03afb6c66b3e93b8fd7eb9b1d8095b0632bd48cb062879cf445e3b54ce07069ad3087b22 |
33 |
|
34 |
diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild b/sci-biology/cmdock/cmdock-0.1.2.ebuild |
35 |
index aa5a4546b..00934f81c 100644 |
36 |
--- a/sci-biology/cmdock/cmdock-0.1.2.ebuild |
37 |
+++ b/sci-biology/cmdock/cmdock-0.1.2.ebuild |
38 |
@@ -3,34 +3,31 @@ |
39 |
|
40 |
EAPI=7 |
41 |
|
42 |
-PYTHON_COMPAT=( python3_{7..9} pypy3 ) |
43 |
+PYTHON_COMPAT=( python3_{7..10} pypy3 ) |
44 |
DOCS_BUILDER="sphinx" |
45 |
DOCS_AUTODOC=0 |
46 |
-inherit python-r1 docs meson |
47 |
+DOCS_DIR="docs" |
48 |
+inherit python-any-r1 docs meson |
49 |
|
50 |
DESCRIPTION="Program for docking ligands to proteins and nucleic acids" |
51 |
HOMEPAGE="https://gitlab.com/Jukic/cmdock" |
52 |
SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz" |
53 |
S="${WORKDIR}/${PN}-v${PV}" |
54 |
-DOCS_DIR="${S}/docs" |
55 |
|
56 |
LICENSE="LGPL-3" |
57 |
-SLOT="${PV}" |
58 |
+SLOT="0/${PV}" |
59 |
KEYWORDS="~amd64" |
60 |
- |
61 |
IUSE="boinc" |
62 |
-REQUIRED_USE="doc? ( ${PYTHON_REQUIRED_USE} )" |
63 |
|
64 |
-DEPEND=" |
65 |
- dev-cpp/eigen |
66 |
- dev-libs/cxxopts |
67 |
+RDEPEND=" |
68 |
+ dev-lang/perl |
69 |
boinc? ( sci-misc/boinc-wrapper ) |
70 |
- doc? ( ${PYTHON_DEPS} ) |
71 |
" |
72 |
-RDEPEND="${DEPEND} |
73 |
- dev-lang/perl |
74 |
+BDEPEND=" |
75 |
+ dev-cpp/eigen:3 |
76 |
+ dev-cpp/pcg-cpp |
77 |
+ dev-libs/cxxopts |
78 |
" |
79 |
-BDEPEND="dev-cpp/pcg-cpp" |
80 |
|
81 |
src_prepare() { |
82 |
default |
83 |
@@ -55,12 +52,12 @@ src_install() { |
84 |
|
85 |
if use boinc ; then |
86 |
insinto /var/lib/boinc/projects/www.sidock.si_sidock |
87 |
- doins "${FILESDIR}/app_info.xml" |
88 |
+ newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml |
89 |
doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml" |
90 |
doins "${FILESDIR}/cmdock-boinc-zip_job_${PV}.xml" |
91 |
|
92 |
- dosym "${EPREFIX}"/usr/bin/boinc-wrapper "/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}" |
93 |
- dosym "${EPREFIX}"/usr/bin/boinc-wrapper "/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}" |
94 |
+ dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV} |
95 |
+ dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV} |
96 |
fi |
97 |
} |
98 |
|
99 |
|
100 |
diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild |
101 |
similarity index 64% |
102 |
copy from sci-biology/cmdock/cmdock-0.1.2.ebuild |
103 |
copy to sci-biology/cmdock/cmdock-0.1.3.ebuild |
104 |
index aa5a4546b..c4a2da7b4 100644 |
105 |
--- a/sci-biology/cmdock/cmdock-0.1.2.ebuild |
106 |
+++ b/sci-biology/cmdock/cmdock-0.1.3.ebuild |
107 |
@@ -3,37 +3,36 @@ |
108 |
|
109 |
EAPI=7 |
110 |
|
111 |
-PYTHON_COMPAT=( python3_{7..9} pypy3 ) |
112 |
+PYTHON_COMPAT=( python3_{7..10} pypy3 ) |
113 |
DOCS_BUILDER="sphinx" |
114 |
DOCS_AUTODOC=0 |
115 |
-inherit python-r1 docs meson |
116 |
+DOCS_DIR="docs" |
117 |
+inherit python-any-r1 docs meson |
118 |
|
119 |
DESCRIPTION="Program for docking ligands to proteins and nucleic acids" |
120 |
HOMEPAGE="https://gitlab.com/Jukic/cmdock" |
121 |
SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz" |
122 |
S="${WORKDIR}/${PN}-v${PV}" |
123 |
-DOCS_DIR="${S}/docs" |
124 |
|
125 |
LICENSE="LGPL-3" |
126 |
-SLOT="${PV}" |
127 |
+SLOT="0/${PV}" |
128 |
KEYWORDS="~amd64" |
129 |
- |
130 |
IUSE="boinc" |
131 |
-REQUIRED_USE="doc? ( ${PYTHON_REQUIRED_USE} )" |
132 |
|
133 |
-DEPEND=" |
134 |
- dev-cpp/eigen |
135 |
- dev-libs/cxxopts |
136 |
+RDEPEND=" |
137 |
+ dev-lang/perl |
138 |
boinc? ( sci-misc/boinc-wrapper ) |
139 |
- doc? ( ${PYTHON_DEPS} ) |
140 |
" |
141 |
-RDEPEND="${DEPEND} |
142 |
- dev-lang/perl |
143 |
+BDEPEND=" |
144 |
+ dev-cpp/eigen:3 |
145 |
+ dev-cpp/indicators |
146 |
+ dev-cpp/pcg-cpp |
147 |
+ dev-libs/cxxopts |
148 |
" |
149 |
-BDEPEND="dev-cpp/pcg-cpp" |
150 |
|
151 |
src_prepare() { |
152 |
default |
153 |
+ rm -r include/indicators || die |
154 |
sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep = declare_dependency(include_directories: '/usr/include')|" -i meson.build || die |
155 |
} |
156 |
|
157 |
@@ -55,12 +54,14 @@ src_install() { |
158 |
|
159 |
if use boinc ; then |
160 |
insinto /var/lib/boinc/projects/www.sidock.si_sidock |
161 |
- doins "${FILESDIR}/app_info.xml" |
162 |
+ newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml |
163 |
doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml" |
164 |
- doins "${FILESDIR}/cmdock-boinc-zip_job_${PV}.xml" |
165 |
+ doins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml" |
166 |
+ newins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml" cmdock-boinc-zip_job_${PV}.xml |
167 |
|
168 |
- dosym "${EPREFIX}"/usr/bin/boinc-wrapper "/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}" |
169 |
- dosym "${EPREFIX}"/usr/bin/boinc-wrapper "/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}" |
170 |
+ dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV} |
171 |
+ dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV} |
172 |
+ dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV} |
173 |
fi |
174 |
} |
175 |
|
176 |
|
177 |
diff --git a/sci-biology/cmdock/files/app_info.xml b/sci-biology/cmdock/files/app_info_0.1.2.xml |
178 |
similarity index 97% |
179 |
rename from sci-biology/cmdock/files/app_info.xml |
180 |
rename to sci-biology/cmdock/files/app_info_0.1.2.xml |
181 |
index eb222052b..f7575656b 100644 |
182 |
--- a/sci-biology/cmdock/files/app_info.xml |
183 |
+++ b/sci-biology/cmdock/files/app_info_0.1.2.xml |
184 |
@@ -47,7 +47,7 @@ |
185 |
</app_version> |
186 |
<app_version> |
187 |
<app_name>cmdock-boinc-zip</app_name> |
188 |
- <version_num>200</version_num> |
189 |
+ <version_num>204</version_num> |
190 |
<file_ref> |
191 |
<file_name>cmdock-boinc-zip_wrapper_0.1.2</file_name> |
192 |
<main_program/> |
193 |
|
194 |
diff --git a/sci-biology/cmdock/files/app_info_0.1.3.xml b/sci-biology/cmdock/files/app_info_0.1.3.xml |
195 |
new file mode 100644 |
196 |
index 000000000..5c901eba8 |
197 |
--- /dev/null |
198 |
+++ b/sci-biology/cmdock/files/app_info_0.1.3.xml |
199 |
@@ -0,0 +1,95 @@ |
200 |
+<app_info> |
201 |
+<app> |
202 |
+ <name>cmdock-boinc</name> |
203 |
+ <user_friendly_name>CurieMarieDock on BOINC</user_friendly_name> |
204 |
+</app> |
205 |
+<app> |
206 |
+ <name>cmdock-boinc-zip</name> |
207 |
+ <user_friendly_name>CurieMarieDock on BOINC + zipped input</user_friendly_name> |
208 |
+</app> |
209 |
+<app> |
210 |
+ <name>cmdock-boinc-zcp</name> |
211 |
+ <user_friendly_name>CurieMarieDock on BOINC + zipped input, checkpoints and progress bar</user_friendly_name> |
212 |
+</app> |
213 |
+ |
214 |
+<file_info> |
215 |
+ <name>cmdock-wrapper_0.1.3</name> |
216 |
+ <executable/> |
217 |
+</file_info> |
218 |
+<file_info> |
219 |
+ <name>cmdock-boinc-zcp_wrapper_0.1.3</name> |
220 |
+ <executable/> |
221 |
+</file_info> |
222 |
+<file_info> |
223 |
+ <name>cmdock-boinc-zip_wrapper_0.1.3</name> |
224 |
+ <executable/> |
225 |
+</file_info> |
226 |
+ |
227 |
+<file_info> |
228 |
+ <name>cmdock-boinc_job_0.1.3.xml</name> |
229 |
+</file_info> |
230 |
+<file_info> |
231 |
+ <name>cmdock-boinc-zcp_job_0.1.3.xml</name> |
232 |
+</file_info> |
233 |
+<file_info> |
234 |
+ <name>cmdock-boinc-zip_job_0.1.3.xml</name> |
235 |
+</file_info> |
236 |
+<file_info> |
237 |
+ <name>docking_out.sd</name> |
238 |
+</file_info> |
239 |
+ |
240 |
+<app_version> |
241 |
+ <app_name>cmdock-boinc</app_name> |
242 |
+ <version_num>103</version_num> |
243 |
+ <file_ref> |
244 |
+ <file_name>cmdock-wrapper_0.1.3</file_name> |
245 |
+ <main_program/> |
246 |
+ </file_ref> |
247 |
+ <file_ref> |
248 |
+ <file_name>cmdock-boinc_job_0.1.3.xml</file_name> |
249 |
+ <open_name>job.xml</open_name> |
250 |
+ <copy_file/> |
251 |
+ </file_ref> |
252 |
+ <file_ref> |
253 |
+ <file_name>docking_out.sd</file_name> |
254 |
+ <open_name>docking_out.sd</open_name> |
255 |
+ <copy_file/> |
256 |
+ </file_ref> |
257 |
+</app_version> |
258 |
+<app_version> |
259 |
+ <app_name>cmdock-boinc-zcp</app_name> |
260 |
+ <version_num>100</version_num> |
261 |
+ <file_ref> |
262 |
+ <file_name>cmdock-boinc-zcp_wrapper_0.1.3</file_name> |
263 |
+ <main_program/> |
264 |
+ </file_ref> |
265 |
+ <file_ref> |
266 |
+ <file_name>cmdock-boinc-zcp_job_0.1.3.xml</file_name> |
267 |
+ <open_name>job.xml</open_name> |
268 |
+ <copy_file/> |
269 |
+ </file_ref> |
270 |
+ <file_ref> |
271 |
+ <file_name>docking_out.sd</file_name> |
272 |
+ <open_name>docking_out.sd</open_name> |
273 |
+ <copy_file/> |
274 |
+ </file_ref> |
275 |
+</app_version> |
276 |
+<app_version> |
277 |
+ <app_name>cmdock-boinc-zip</app_name> |
278 |
+ <version_num>300</version_num> |
279 |
+ <file_ref> |
280 |
+ <file_name>cmdock-boinc-zip_wrapper_0.1.3</file_name> |
281 |
+ <main_program/> |
282 |
+ </file_ref> |
283 |
+ <file_ref> |
284 |
+ <file_name>cmdock-boinc-zip_job_0.1.3.xml</file_name> |
285 |
+ <open_name>job.xml</open_name> |
286 |
+ <copy_file/> |
287 |
+ </file_ref> |
288 |
+ <file_ref> |
289 |
+ <file_name>docking_out.sd</file_name> |
290 |
+ <open_name>docking_out.sd</open_name> |
291 |
+ <copy_file/> |
292 |
+ </file_ref> |
293 |
+</app_version> |
294 |
+</app_info> |
295 |
|
296 |
diff --git a/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml |
297 |
new file mode 100644 |
298 |
index 000000000..3c7818151 |
299 |
--- /dev/null |
300 |
+++ b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml |
301 |
@@ -0,0 +1,15 @@ |
302 |
+<job_desc> |
303 |
+ <task> |
304 |
+ <application>/opt/cmdock-0.1.3/build/cmdock</application> |
305 |
+ <stdout_filename>docking_log</stdout_filename> |
306 |
+ <command_line>-c -j 1 -r target.prm -p /opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line> |
307 |
+ <checkpoint_filename>docking_out.chk</checkpoint_filename> |
308 |
+ <fraction_done_filename>docking_out.progress</fraction_done_filename> |
309 |
+ <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.3</setenv> |
310 |
+ <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv> |
311 |
+ <setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv> |
312 |
+ </task> |
313 |
+ <unzip_input> |
314 |
+ <zipfilename>ligands.zip</zipfilename> |
315 |
+ </unzip_input> |
316 |
+</job_desc> |
317 |
|
318 |
diff --git a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml |
319 |
index 2691d09ea..a11f1fe9b 100644 |
320 |
--- a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml |
321 |
+++ b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml |
322 |
@@ -2,7 +2,8 @@ |
323 |
<task> |
324 |
<application>/opt/cmdock-0.1.2/build/cmdock</application> |
325 |
<stdout_filename>docking_log</stdout_filename> |
326 |
- <command_line>-r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line> |
327 |
+ <command_line>-c -r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line> |
328 |
+ <checkpoint_filename>docking_out.chk</checkpoint_filename> |
329 |
<setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv> |
330 |
<setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH</setenv> |
331 |
<setenv>PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB</setenv> |
332 |
|
333 |
diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml |
334 |
new file mode 100644 |
335 |
index 000000000..6082dc8fe |
336 |
--- /dev/null |
337 |
+++ b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml |
338 |
@@ -0,0 +1,10 @@ |
339 |
+<job_desc> |
340 |
+ <task> |
341 |
+ <application>/opt/cmdock-0.1.3/build/cmdock</application> |
342 |
+ <stdout_filename>docking_log</stdout_filename> |
343 |
+ <command_line>-r target.prm -p /opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line> |
344 |
+ <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.3</setenv> |
345 |
+ <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv> |
346 |
+ <setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv> |
347 |
+ </task> |
348 |
+</job_desc> |