commit: aba20d3142c80878bbc1a3b045f14c849a63cb63
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Sat May 29 13:37:10 2021 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Sat May 29 15:48:30 2021 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=aba20d31
sci-biology/cmdock: add 0.1.3
* revise deps
* fix symlinks
* replace slotting with subslotting
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/Manifest | 1 +
sci-biology/cmdock/cmdock-0.1.2.ebuild | 29 +++----
.../{cmdock-0.1.2.ebuild => cmdock-0.1.3.ebuild} | 35 ++++----
.../files/{app_info.xml => app_info_0.1.2.xml} | 2 +-
sci-biology/cmdock/files/app_info_0.1.3.xml | 95 ++++++++++++++++++++++
.../cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml | 15 ++++
.../cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 3 +-
.../cmdock/files/cmdock-boinc_job_0.1.3.xml | 10 +++
8 files changed, 155 insertions(+), 35 deletions(-)
diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
index 25663d438..c20f5e305 100644
--- a/sci-biology/cmdock/Manifest
+++ b/sci-biology/cmdock/Manifest
@@ -1 +1,2 @@
DIST cmdock-v0.1.2.tar.gz 13394195 BLAKE2B
bd377b6a953d1e38b527da4eda36aee7a634e9f0c400487d4092ae1939589890038fc90052d8bddb25457dd027fa929acd50e836d65bd5994af89116f4c770a7
SHA512
90d4114a10dde99d34cd7ea4b28399da744cc295adebb10f1f9771b59841cd13e07cae5218643c90dd2847cdb014867ab795649a3d1883396a3609c3344b8226
+DIST cmdock-v0.1.3.tar.gz 13416412 BLAKE2B
abd6382943fb2ca2459fa493f8025e335821b96a95b88267dd493c28cd3280481b41ec6480fd3514cff126ab1077e89f075e5311393b1cd366403419e9c47454
SHA512
d941b672d14bad4fda4eaeb7aa313da1ade213241a1aee392747943a03afb6c66b3e93b8fd7eb9b1d8095b0632bd48cb062879cf445e3b54ce07069ad3087b22
diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild
b/sci-biology/cmdock/cmdock-0.1.2.ebuild
index aa5a4546b..00934f81c 100644
--- a/sci-biology/cmdock/cmdock-0.1.2.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.2.ebuild
@@ -3,34 +3,31 @@
EAPI=7
-PYTHON_COMPAT=( python3_{7..9} pypy3 )
+PYTHON_COMPAT=( python3_{7..10} pypy3 )
DOCS_BUILDER="sphinx"
DOCS_AUTODOC=0
-inherit python-r1 docs meson
+DOCS_DIR="docs"
+inherit python-any-r1 docs meson
DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
HOMEPAGE="https://gitlab.com/Jukic/cmdock";
SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz";
S="${WORKDIR}/${PN}-v${PV}"
-DOCS_DIR="${S}/docs"
LICENSE="LGPL-3"
-SLOT="${PV}"
+SLOT="0/${PV}"
KEYWORDS="~amd64"
-
IUSE="boinc"
-REQUIRED_USE="doc? ( ${PYTHON_REQUIRED_USE} )"
-DEPEND="
- dev-cpp/eigen
- dev-libs/cxxopts
+RDEPEND="
+ dev-lang/perl
boinc? ( sci-misc/boinc-wrapper )
- doc? ( ${PYTHON_DEPS} )
"
-RDEPEND="${DEPEND}
- dev-lang/perl
+BDEPEND="
+ dev-cpp/eigen:3
+ dev-cpp/pcg-cpp
+ dev-libs/cxxopts
"
-BDEPEND="dev-cpp/pcg-cpp"
src_prepare() {
default
@@ -55,12 +52,12 @@ src_install() {
if use boinc ; then
insinto /var/lib/boinc/projects/www.sidock.si_sidock
- doins "${FILESDIR}/app_info.xml"
+ newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml
doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml"
doins "${FILESDIR}/cmdock-boinc-zip_job_${PV}.xml"
- dosym "${EPREFIX}"/usr/bin/boinc-wrapper
"/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}"
- dosym "${EPREFIX}"/usr/bin/boinc-wrapper
"/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}"
+ dosym ../../../../../usr/bin/boinc-wrapper
/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}
+ dosym ../../../../../usr/bin/boinc-wrapper
/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}
fi
}
diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild
b/sci-biology/cmdock/cmdock-0.1.3.ebuild
similarity index 64%
copy from sci-biology/cmdock/cmdock-0.1.2.ebuild
copy to sci-biology/cmdock/cmdock-0.1.3.ebuild
index aa5a4546b..c4a2da7b4 100644
--- a/sci-biology/cmdock/cmdock-0.1.2.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.3.ebuild
@@ -3,37 +3,36 @@
EAPI=7
-PYTHON_COMPAT=( python3_{7..9} pypy3 )
+PYTHON_COMPAT=( python3_{7..10} pypy3 )
DOCS_BUILDER="sphinx"
DOCS_AUTODOC=0
-inherit python-r1 docs meson
+DOCS_DIR="docs"
+inherit python-any-r1 docs meson
DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
HOMEPAGE="https://gitlab.com/Jukic/cmdock";
SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz";
S="${WORKDIR}/${PN}-v${PV}"
-DOCS_DIR="${S}/docs"
LICENSE="LGPL-3"
-SLOT="${PV}"
+SLOT="0/${PV}"
KEYWORDS="~amd64"
-
IUSE="boinc"
-REQUIRED_USE="doc? ( ${PYTHON_REQUIRED_USE} )"
-DEPEND="
- dev-cpp/eigen
- dev-libs/cxxopts
+RDEPEND="
+ dev-lang/perl
boinc? ( sci-misc/boinc-wrapper )
- doc? ( ${PYTHON_DEPS} )
"
-RDEPEND="${DEPEND}
- dev-lang/perl
+BDEPEND="
+ dev-cpp/eigen:3
+ dev-cpp/indicators
+ dev-cpp/pcg-cpp
+ dev-libs/cxxopts
"
-BDEPEND="dev-cpp/pcg-cpp"
src_prepare() {
default
+ rm -r include/indicators || die
sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep =
declare_dependency(include_directories: '/usr/include')|" -i meson.build || die
}
@@ -55,12 +54,14 @@ src_install() {
if use boinc ; then
insinto /var/lib/boinc/projects/www.sidock.si_sidock
- doins "${FILESDIR}/app_info.xml"
+ newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml
doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml"
- doins "${FILESDIR}/cmdock-boinc-zip_job_${PV}.xml"
+ doins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml"
+ newins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml"
cmdock-boinc-zip_job_${PV}.xml
- dosym "${EPREFIX}"/usr/bin/boinc-wrapper
"/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}"
- dosym "${EPREFIX}"/usr/bin/boinc-wrapper
"/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}"
+ dosym ../../../../../usr/bin/boinc-wrapper
/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}
+ dosym ../../../../../usr/bin/boinc-wrapper
/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV}
+ dosym ../../../../../usr/bin/boinc-wrapper
/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}
fi
}
diff --git a/sci-biology/cmdock/files/app_info.xml
b/sci-biology/cmdock/files/app_info_0.1.2.xml
similarity index 97%
rename from sci-biology/cmdock/files/app_info.xml
rename to sci-biology/cmdock/files/app_info_0.1.2.xml
index eb222052b..f7575656b 100644
--- a/sci-biology/cmdock/files/app_info.xml
+++ b/sci-biology/cmdock/files/app_info_0.1.2.xml
@@ -47,7 +47,7 @@
</app_version>
<app_version>
<app_name>cmdock-boinc-zip</app_name>
- <version_num>200</version_num>
+ <version_num>204</version_num>
<file_ref>
<file_name>cmdock-boinc-zip_wrapper_0.1.2</file_name>
<main_program/>
diff --git a/sci-biology/cmdock/files/app_info_0.1.3.xml
b/sci-biology/cmdock/files/app_info_0.1.3.xml
new file mode 100644
index 000000000..5c901eba8
--- /dev/null
+++ b/sci-biology/cmdock/files/app_info_0.1.3.xml
@@ -0,0 +1,95 @@
+<app_info>
+<app>
+ <name>cmdock-boinc</name>
+ <user_friendly_name>CurieMarieDock on BOINC</user_friendly_name>
+</app>
+<app>
+ <name>cmdock-boinc-zip</name>
+ <user_friendly_name>CurieMarieDock on BOINC + zipped
input</user_friendly_name>
+</app>
+<app>
+ <name>cmdock-boinc-zcp</name>
+ <user_friendly_name>CurieMarieDock on BOINC + zipped input, checkpoints
and progress bar</user_friendly_name>
+</app>
+
+<file_info>
+ <name>cmdock-wrapper_0.1.3</name>
+ <executable/>
+</file_info>
+<file_info>
+ <name>cmdock-boinc-zcp_wrapper_0.1.3</name>
+ <executable/>
+</file_info>
+<file_info>
+ <name>cmdock-boinc-zip_wrapper_0.1.3</name>
+ <executable/>
+</file_info>
+
+<file_info>
+ <name>cmdock-boinc_job_0.1.3.xml</name>
+</file_info>
+<file_info>
+ <name>cmdock-boinc-zcp_job_0.1.3.xml</name>
+</file_info>
+<file_info>
+ <name>cmdock-boinc-zip_job_0.1.3.xml</name>
+</file_info>
+<file_info>
+ <name>docking_out.sd</name>
+</file_info>
+
+<app_version>
+ <app_name>cmdock-boinc</app_name>
+ <version_num>103</version_num>
+ <file_ref>
+ <file_name>cmdock-wrapper_0.1.3</file_name>
+ <main_program/>
+ </file_ref>
+ <file_ref>
+ <file_name>cmdock-boinc_job_0.1.3.xml</file_name>
+ <open_name>job.xml</open_name>
+ <copy_file/>
+ </file_ref>
+ <file_ref>
+ <file_name>docking_out.sd</file_name>
+ <open_name>docking_out.sd</open_name>
+ <copy_file/>
+ </file_ref>
+</app_version>
+<app_version>
+ <app_name>cmdock-boinc-zcp</app_name>
+ <version_num>100</version_num>
+ <file_ref>
+ <file_name>cmdock-boinc-zcp_wrapper_0.1.3</file_name>
+ <main_program/>
+ </file_ref>
+ <file_ref>
+ <file_name>cmdock-boinc-zcp_job_0.1.3.xml</file_name>
+ <open_name>job.xml</open_name>
+ <copy_file/>
+ </file_ref>
+ <file_ref>
+ <file_name>docking_out.sd</file_name>
+ <open_name>docking_out.sd</open_name>
+ <copy_file/>
+ </file_ref>
+</app_version>
+<app_version>
+ <app_name>cmdock-boinc-zip</app_name>
+ <version_num>300</version_num>
+ <file_ref>
+ <file_name>cmdock-boinc-zip_wrapper_0.1.3</file_name>
+ <main_program/>
+ </file_ref>
+ <file_ref>
+ <file_name>cmdock-boinc-zip_job_0.1.3.xml</file_name>
+ <open_name>job.xml</open_name>
+ <copy_file/>
+ </file_ref>
+ <file_ref>
+ <file_name>docking_out.sd</file_name>
+ <open_name>docking_out.sd</open_name>
+ <copy_file/>
+ </file_ref>
+</app_version>
+</app_info>
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
new file mode 100644
index 000000000..3c7818151
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
@@ -0,0 +1,15 @@
+<job_desc>
+ <task>
+ <application>/opt/cmdock-0.1.3/build/cmdock</application>
+ <stdout_filename>docking_log</stdout_filename>
+ <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>
+ <checkpoint_filename>docking_out.chk</checkpoint_filename>
+
<fraction_done_filename>docking_out.progress</fraction_done_filename>
+ <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.3</setenv>
+
<setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv>
+ <setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv>
+ </task>
+ <unzip_input>
+ <zipfilename>ligands.zip</zipfilename>
+ </unzip_input>
+</job_desc>
diff --git a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
index 2691d09ea..a11f1fe9b 100644
--- a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
+++ b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
@@ -2,7 +2,8 @@
<task>
<application>/opt/cmdock-0.1.2/build/cmdock</application>
<stdout_filename>docking_log</stdout_filename>
- <command_line>-r target.prm -p
/opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o
docking_out</command_line>
+ <command_line>-c -r target.prm -p
/opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o
docking_out</command_line>
+ <checkpoint_filename>docking_out.chk</checkpoint_filename>
<setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv>
<setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH</setenv>
<setenv>PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB</setenv>
diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
new file mode 100644
index 000000000..6082dc8fe
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
@@ -0,0 +1,10 @@
+<job_desc>
+ <task>
+ <application>/opt/cmdock-0.1.3/build/cmdock</application>
+ <stdout_filename>docking_log</stdout_filename>
+ <command_line>-r target.prm -p
/opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o
docking_out</command_line>
+ <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.3</setenv>
+
<setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv>
+ <setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv>
+ </task>
+</job_desc>
