* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/files/, sci-biology/cmdock/
@ 2021-05-18 21:31 Anna Vyalkova
0 siblings, 0 replies; 4+ messages in thread
From: Anna Vyalkova @ 2021-05-18 21:31 UTC (permalink / raw
To: gentoo-commits
commit: 8b0e3834b1db271f7499bfb1721eeb2d74b0907a
Author: Anna Vyalkova <cyber <AT> sysrq <DOT> in>
AuthorDate: Tue May 18 21:31:09 2021 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Tue May 18 21:31:18 2021 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=8b0e3834
sci-biology/cmdock: initial import
Signed-off-by: Anna Vyalkova <cyber <AT> sysrq.in>
sci-biology/cmdock/Manifest | 1 +
sci-biology/cmdock/cmdock-0.1.2.ebuild | 74 ++++++++++++++++++++++
sci-biology/cmdock/files/app_config.xml | 66 +++++++++++++++++++
.../cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 13 ++++
.../cmdock/files/cmdock-boinc_job_0.1.2.xml | 10 +++
sci-biology/cmdock/metadata.xml | 17 +++++
6 files changed, 181 insertions(+)
diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
new file mode 100644
index 000000000..25663d438
--- /dev/null
+++ b/sci-biology/cmdock/Manifest
@@ -0,0 +1 @@
+DIST cmdock-v0.1.2.tar.gz 13394195 BLAKE2B bd377b6a953d1e38b527da4eda36aee7a634e9f0c400487d4092ae1939589890038fc90052d8bddb25457dd027fa929acd50e836d65bd5994af89116f4c770a7 SHA512 90d4114a10dde99d34cd7ea4b28399da744cc295adebb10f1f9771b59841cd13e07cae5218643c90dd2847cdb014867ab795649a3d1883396a3609c3344b8226
diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild b/sci-biology/cmdock/cmdock-0.1.2.ebuild
new file mode 100644
index 000000000..34c37a5ee
--- /dev/null
+++ b/sci-biology/cmdock/cmdock-0.1.2.ebuild
@@ -0,0 +1,74 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7..9} pypy3 )
+DOCS_BUILDER="sphinx"
+DOCS_AUTODOC=0
+inherit python-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="${PV}"
+KEYWORDS="~amd64"
+IUSE="boinc"
+
+DEPEND="
+ dev-cpp/eigen
+ dev-libs/cxxopts
+ boinc? ( sci-misc/boinc-wrapper )
+"
+RDEPEND="${DEPEND}
+ dev-lang/perl
+"
+BDEPEND="dev-cpp/pcg-cpp"
+
+src_prepare() {
+ default
+ sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep = declare_dependency(include_directories: '/usr/include')|" -i meson.build || die
+}
+
+src_configure() {
+ # very weird directory layout
+ local emesonargs=(
+ --prefix="${EPREFIX}/opt/cmdock-${PV}"
+ )
+ meson_src_configure
+}
+
+src_compile() {
+ meson_src_compile
+ docs_compile
+}
+
+src_install() {
+ meson_src_install
+
+ if use boinc ; then
+ insinto /var/lib/boinc/projects/www.sidock.si_sidock
+ doins "${FILESDIR}/app_config.xml"
+ doins "${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}"
+ fi
+}
+
+pkg_postinst() {
+ if use boinc ; then
+ touch /var/lib/boinc/projects/www.sidock.si_sidock/docking_out.sd || die
+ elog
+ elog "The easiest way to do something useful with this application"
+ elog "is to attach it to SiDock@home BOINC project."
+ elog
+ elog "- Master URL: https://sidock.si/sidock/"
+ elog "- Invitation code: Crunch_4Science"
+ fi
+}
diff --git a/sci-biology/cmdock/files/app_config.xml b/sci-biology/cmdock/files/app_config.xml
new file mode 100644
index 000000000..6a41b0bb2
--- /dev/null
+++ b/sci-biology/cmdock/files/app_config.xml
@@ -0,0 +1,66 @@
+<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>
+
+<file_info>
+ <name>cmdock-wrapper_0.1.2</name>
+ <executable/>
+</file_info>
+<file_info>
+ <name>cmdock-boinc-zip_wrapper_0.1.2</name>
+ <executable/>
+</file_info>
+
+<file_info>
+ <name>cmdock-boinc_job_0.1.2.xml</name>
+</file_info>
+<file_info>
+ <name>cmdock-boinc-zip_job_0.1.2.xml</name>
+</file_info>
+<file_info>
+ <name>docking_out.sd</name>
+</file_info>
+
+<app_version>
+ <app_name>cmdock-boinc</app_name>
+ <version_num>102</version_num>
+ <file_ref>
+ <file_name>cmdock-wrapper_0.1.2</file_name>
+ <main_program/>
+ </file_ref>
+ <file_ref>
+ <file_name>cmdock-boinc_job_0.1.2.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>100</version_num>
+ <file_ref>
+ <file_name>cmdock-boinc-zip_wrapper_0.1.2</file_name>
+ <main_program/>
+ </file_ref>
+ <file_ref>
+ <file_name>cmdock-boinc-zip_job_0.1.2.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-zip_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
new file mode 100644
index 000000000..3b89cdfd2
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
@@ -0,0 +1,13 @@
+<job_desc>
+ <task>
+ <application>/opt/cmdock/build/cmdock-0.1.2</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>
+ <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:$PERL5LIB</setenv>
+ </task>
+ <unzip_input>
+ <zipfilename>ligands.zip</zipfilename>
+ </unzip_input>
+</job_desc>
diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
new file mode 100644
index 000000000..aa3042498
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
@@ -0,0 +1,10 @@
+<job_desc>
+ <task>
+ <application>/opt/cmdock/build/cmdock-0.1.2</application>
+ <stdout_filename>docking_log</stdout_filename>
+ <command_line>-r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+ <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv>
+ <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH</setenv>
+ <setenv>PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB</setenv>
+ </task>
+</job_desc>
diff --git a/sci-biology/cmdock/metadata.xml b/sci-biology/cmdock/metadata.xml
new file mode 100644
index 000000000..9bb734387
--- /dev/null
+++ b/sci-biology/cmdock/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <upstream>
+ <remote-id type="gitlab">Jukic/cmdock</remote-id>
+ <bugs-to>https://gitlab.com/Jukic/cmdock/-/issues</bugs-to>
+ </upstream>
+ <maintainer type="person">
+ <email>cyber+gentoo@sysrq.in</email>
+ <name>Anna</name>
+ </maintainer>
+ <use>
+ <flag name="boinc">
+ Use CmDock with SiDock@home BOINC project
+ </flag>
+ </use>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/files/, sci-biology/cmdock/
@ 2021-07-01 5:08 Anna Vyalkova
0 siblings, 0 replies; 4+ messages in thread
From: Anna Vyalkova @ 2021-07-01 5:08 UTC (permalink / raw
To: gentoo-commits
commit: eb972dae4900efd571efe420cf683200a997d924
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Sun Jun 27 08:51:43 2021 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Thu Jul 1 04:58:25 2021 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=eb972dae
sci-biology/cmdock: drop obsolete
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/Manifest | 1 -
sci-biology/cmdock/cmdock-0.1.2.ebuild | 74 ----------------------
sci-biology/cmdock/cmdock-0.1.3.ebuild | 13 ++--
sci-biology/cmdock/files/app_info_0.1.2.xml | 66 -------------------
sci-biology/cmdock/files/app_info_0.1.3.xml | 58 -----------------
.../cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 14 ----
.../cmdock/files/cmdock-boinc_job_0.1.2.xml | 10 ---
.../cmdock/files/cmdock-boinc_job_0.1.3.xml | 10 ---
8 files changed, 4 insertions(+), 242 deletions(-)
diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
index c20f5e305..84968a8f8 100644
--- a/sci-biology/cmdock/Manifest
+++ b/sci-biology/cmdock/Manifest
@@ -1,2 +1 @@
-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
deleted file mode 100644
index 00934f81c..000000000
--- a/sci-biology/cmdock/cmdock-0.1.2.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..10} pypy3 )
-DOCS_BUILDER="sphinx"
-DOCS_AUTODOC=0
-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}"
-
-LICENSE="LGPL-3"
-SLOT="0/${PV}"
-KEYWORDS="~amd64"
-IUSE="boinc"
-
-RDEPEND="
- dev-lang/perl
- boinc? ( sci-misc/boinc-wrapper )
-"
-BDEPEND="
- dev-cpp/eigen:3
- dev-cpp/pcg-cpp
- dev-libs/cxxopts
-"
-
-src_prepare() {
- default
- sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep = declare_dependency(include_directories: '/usr/include')|" -i meson.build || die
-}
-
-src_configure() {
- # very weird directory layout
- local emesonargs=(
- --prefix="${EPREFIX}/opt/cmdock-${PV}"
- )
- meson_src_configure
-}
-
-src_compile() {
- meson_src_compile
- docs_compile
-}
-
-src_install() {
- meson_src_install
-
- if use boinc ; then
- insinto /var/lib/boinc/projects/www.sidock.si_sidock
- newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml
- doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml"
- doins "${FILESDIR}/cmdock-boinc-zip_job_${PV}.xml"
-
- dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}
- dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}
- fi
-}
-
-pkg_postinst() {
- if use boinc ; then
- touch /var/lib/boinc/projects/www.sidock.si_sidock/docking_out.sd || die
- elog
- elog "The easiest way to do something useful with this application"
- elog "is to attach it to SiDock@home BOINC project."
- elog
- elog "- Master URL: https://sidock.si/sidock/"
- elog "- Invitation code: Crunch_4Science"
- fi
-}
diff --git a/sci-biology/cmdock/cmdock-0.1.3.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild
index c4a2da7b4..e42b1f253 100644
--- a/sci-biology/cmdock/cmdock-0.1.3.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.3.ebuild
@@ -1,9 +1,9 @@
# Copyright 2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..10} pypy3 )
+PYTHON_COMPAT=( python3_{8..10} pypy3 )
DOCS_BUILDER="sphinx"
DOCS_AUTODOC=0
DOCS_DIR="docs"
@@ -26,14 +26,13 @@ RDEPEND="
BDEPEND="
dev-cpp/eigen:3
dev-cpp/indicators
- dev-cpp/pcg-cpp
+ >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
dev-libs/cxxopts
"
src_prepare() {
default
rm -r include/indicators || die
- sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep = declare_dependency(include_directories: '/usr/include')|" -i meson.build || die
}
src_configure() {
@@ -55,13 +54,9 @@ src_install() {
if use boinc ; then
insinto /var/lib/boinc/projects/www.sidock.si_sidock
newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml
- doins "${FILESDIR}/cmdock-boinc_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 ../../../../../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_${PV}
+ dosym -r /usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV}
fi
}
diff --git a/sci-biology/cmdock/files/app_info_0.1.2.xml b/sci-biology/cmdock/files/app_info_0.1.2.xml
deleted file mode 100644
index f7575656b..000000000
--- a/sci-biology/cmdock/files/app_info_0.1.2.xml
+++ /dev/null
@@ -1,66 +0,0 @@
-<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>
-
-<file_info>
- <name>cmdock-wrapper_0.1.2</name>
- <executable/>
-</file_info>
-<file_info>
- <name>cmdock-boinc-zip_wrapper_0.1.2</name>
- <executable/>
-</file_info>
-
-<file_info>
- <name>cmdock-boinc_job_0.1.2.xml</name>
-</file_info>
-<file_info>
- <name>cmdock-boinc-zip_job_0.1.2.xml</name>
-</file_info>
-<file_info>
- <name>docking_out.sd</name>
-</file_info>
-
-<app_version>
- <app_name>cmdock-boinc</app_name>
- <version_num>102</version_num>
- <file_ref>
- <file_name>cmdock-wrapper_0.1.2</file_name>
- <main_program/>
- </file_ref>
- <file_ref>
- <file_name>cmdock-boinc_job_0.1.2.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>204</version_num>
- <file_ref>
- <file_name>cmdock-boinc-zip_wrapper_0.1.2</file_name>
- <main_program/>
- </file_ref>
- <file_ref>
- <file_name>cmdock-boinc-zip_job_0.1.2.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/app_info_0.1.3.xml b/sci-biology/cmdock/files/app_info_0.1.3.xml
index 5c901eba8..162ad0c05 100644
--- a/sci-biology/cmdock/files/app_info_0.1.3.xml
+++ b/sci-biology/cmdock/files/app_info_0.1.3.xml
@@ -1,61 +1,21 @@
<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>
@@ -74,22 +34,4 @@
<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-zip_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
deleted file mode 100644
index a11f1fe9b..000000000
--- a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<job_desc>
- <task>
- <application>/opt/cmdock-0.1.2/build/cmdock</application>
- <stdout_filename>docking_log</stdout_filename>
- <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>
- </task>
- <unzip_input>
- <zipfilename>ligands.zip</zipfilename>
- </unzip_input>
-</job_desc>
diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
deleted file mode 100644
index c670b677e..000000000
--- a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<job_desc>
- <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>
- <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>
- </task>
-</job_desc>
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
deleted file mode 100644
index 6082dc8fe..000000000
--- a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<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>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/files/, sci-biology/cmdock/
@ 2023-01-07 9:41 Anna Vyalkova
0 siblings, 0 replies; 4+ messages in thread
From: Anna Vyalkova @ 2023-01-07 9:41 UTC (permalink / raw
To: gentoo-commits
commit: 43200432ac81cfb799df3a1a62076920d42f8f5a
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Fri Jan 6 05:30:16 2023 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Sat Jan 7 09:40:44 2023 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=43200432
sci-biology/cmdock: add 0.2.0
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/Manifest | 1 +
sci-biology/cmdock/cmdock-0.2.0.ebuild | 112 ++++++++++++++++++++++++
sci-biology/cmdock/files/app_info_0.2.0.xml | 50 +++++++++++
sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml | 15 ++++
4 files changed, 178 insertions(+)
diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
index 5f5d12c7f..8757cee0d 100644
--- a/sci-biology/cmdock/Manifest
+++ b/sci-biology/cmdock/Manifest
@@ -1 +1,2 @@
DIST cmdock-v0.1.4.tar.bz2 14095825 BLAKE2B 80d5d86dc11e842689255d2b673545436404fb92815bb33b5ff15eba0cd3e8970a750dfeb657d018ef31024a2ecf591bcb5c6c1f427be1d0c86a0cfc017c8aa0 SHA512 d0d9a96ef0fad8cd4b320a2339a1889e481a825c5712259e04c9e91b34de597def3100c3c9f71fa63f3eef43892a17c0114d4cc93e99424bcdcc1fc97c25f51e
+DIST cmdock-v0.2.0.tar.bz2 14155812 BLAKE2B daf2f1ac137761bf24b2295dd025e81b29eefae23b5b33c7319f87cf6ea938bcb2ce619229d84dd2af9f31785b63bab4dda95bba3e7cd4de122f94f953913694 SHA512 67eda7e712650641219d7d4d4f9c455923bc6241aa687c5b3f489e251b9e838c3bcdcc7184540ab28f96ab8f573320599669e4b52989ce33a015bceec89717c5
diff --git a/sci-biology/cmdock/cmdock-0.2.0.ebuild b/sci-biology/cmdock/cmdock-0.2.0.ebuild
new file mode 100644
index 000000000..9a91c85df
--- /dev/null
+++ b/sci-biology/cmdock/cmdock-0.2.0.ebuild
@@ -0,0 +1,112 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+BOINC_APP_OPTIONAL="true"
+inherit boinc-app flag-o-matic meson optfeature python-any-r1
+
+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.bz2"
+S="${WORKDIR}/${PN}-v${PV}"
+
+LICENSE="LGPL-3 ZLIB"
+SLOT="0/${PV}"
+KEYWORDS="~amd64"
+IUSE="apidoc boinc cpu_flags_x86_sse2 doc test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ boinc? ( sci-misc/boinc-wrapper )
+"
+DEPEND="
+ dev-cpp/eigen:3
+ dev-cpp/indicators
+ >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
+ dev-libs/cxxopts
+"
+BDEPEND="
+ apidoc? (
+ app-doc/doxygen
+ dev-texlive/texlive-fontutils
+ )
+ doc? (
+ $(python_gen_any_dep '
+ dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]
+ dev-python/sphinx[${PYTHON_USEDEP}]
+ ')
+ )
+ test? ( ${PYTHON_DEPS} )
+"
+
+DOCS=( README.md changelog.md )
+
+BOINC_MASTER_URL="https://www.sidock.si/sidock/"
+BOINC_INVITATION_CODE="Crunch_4Science"
+BOINC_APP_HELPTEXT=\
+"The easiest way to do something useful with this application
+is to attach it to SiDock@home BOINC project."
+
+INSTALL_PREFIX="${EPREFIX}/opt/${P}"
+
+python_check_deps() {
+ use doc || return 0
+
+ python_has_version "dev-python/sphinx[${PYTHON_USEDEP}]" &&
+ python_has_version "dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]"
+}
+
+foreach_wrapper_job() {
+ sed -e "s:@PREFIX@:${INSTALL_PREFIX}:g" -i "${1}" || die
+}
+
+src_prepare() {
+ default
+ python_fix_shebang "${S}"/bin
+}
+
+src_configure() {
+ # very weird directory layout
+ local emesonargs=(
+ --prefix="${INSTALL_PREFIX}"
+ $(meson_use apidoc)
+ $(meson_use doc)
+ $(meson_use test tests)
+ -Ddocdir="${EPREFIX}"/usr/share/doc/${PF}
+ )
+ meson_src_configure
+
+ use cpu_flags_x86_sse2 || append-cppflags "-DBUNDLE_NO_SSE"
+}
+
+src_install() {
+ meson_src_install
+ python_optimize "${D}${INSTALL_PREFIX}"/bin
+
+ if use boinc; then
+ doappinfo "${FILESDIR}"/app_info_${PV}.xml
+ dowrapper cmdock-l
+
+ # install cmdock executable
+ exeinto "$(get_project_root)"
+ exeopts --owner root --group boinc
+ newexe "${D}${INSTALL_PREFIX}"/bin/cmdock cmdock-${PV}
+
+ # install a blank file
+ touch "${T}"/docking_out || die
+ insinto "$(get_project_root)"
+ insopts --owner root --group boinc
+ doins "${T}"/docking_out
+ fi
+}
+
+pkg_postinst() {
+ optfeature "sdtether.py and sdrmsd.py scripts" "dev-python/numpy sci-chemistry/openbabel[python]"
+ use boinc && boinc-app_pkg_postinst
+}
+
+pkg_postrm() {
+ use boinc && boinc-app_pkg_postrm
+}
diff --git a/sci-biology/cmdock/files/app_info_0.2.0.xml b/sci-biology/cmdock/files/app_info_0.2.0.xml
new file mode 100644
index 000000000..ad23f7890
--- /dev/null
+++ b/sci-biology/cmdock/files/app_info_0.2.0.xml
@@ -0,0 +1,50 @@
+<app_info>
+<app>
+ <name>cmdock-l</name>
+ <user_friendly_name>CurieMarieDock 0.2.0 long tasks</user_friendly_name>
+</app>
+
+<file_info>
+ <name>cmdock-l_wrapper_@PV@</name>
+ <sticky/>
+ <executable/>
+</file_info>
+<file_info>
+ <name>cmdock-@PV@</name>
+ <sticky/>
+ <executable/>
+</file_info>
+
+<file_info>
+ <name>cmdock-l_job_@PV@.xml</name>
+ <sticky/>
+</file_info>
+<file_info>
+ <name>docking_out</name>
+ <sticky/>
+</file_info>
+
+<app_version>
+ <app_name>cmdock-l</app_name>
+ <version_num>100</version_num>
+ <file_ref>
+ <file_name>cmdock-l_wrapper_@PV@</file_name>
+ <main_program/>
+ </file_ref>
+ <file_ref>
+ <file_name>cmdock-@PV@</file_name>
+ <open_name>cmdock</open_name>
+ <copy_file/>
+ </file_ref>
+ <file_ref>
+ <file_name>cmdock-l_job_@PV@.xml</file_name>
+ <open_name>job.xml</open_name>
+ <copy_file/>
+ </file_ref>
+ <file_ref>
+ <file_name>docking_out</file_name>
+ <open_name>docking_out</open_name>
+ <copy_file/>
+ </file_ref>
+</app_version>
+</app_info>
diff --git a/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml b/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml
new file mode 100644
index 000000000..a163eb29c
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml
@@ -0,0 +1,15 @@
+<job_desc>
+ <task>
+ <application>cmdock</application>
+ <stdout_filename>docking_log</stdout_filename>
+ <command_line>-c -j 1 -b 1 -x -r target.prm -p "@PREFIX@/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=@PREFIX@</setenv>
+ <setenv>LD_LIBRARY_PATH=@PREFIX@/lib:$LD_LIBRARY_PATH</setenv>
+ <setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv>
+ </task>
+ <unzip_input>
+ <zipfilename>ligands.zip</zipfilename>
+ </unzip_input>
+</job_desc>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/files/, sci-biology/cmdock/
@ 2024-07-14 7:27 Anna Vyalkova
0 siblings, 0 replies; 4+ messages in thread
From: Anna Vyalkova @ 2024-07-14 7:27 UTC (permalink / raw
To: gentoo-commits
commit: 1a76004eaaa74e01bdbe8f2afacac8306fbe6d6f
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Tue Jul 9 15:56:46 2024 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Sun Jul 14 07:27:19 2024 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=1a76004e
sci-biology/cmdock: boinc fixes
* Update cmdline to the upstream current. Particularly, the option that
causes CmDock to get stuck in an infinite loop in 1-5% of runs is
removed.
* Sync with boinc-app.eclass updates.
Closes: https://bugs.gentoo.org/935231
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
...dock-0.2.0-r1.ebuild => cmdock-0.2.0-r2.ebuild} | 25 +++++++++++-----------
.../{app_info_0.2.0.xml => app_info_0.2.0-r1.xml} | 14 ++++++------
...k-l_job_0.2.0.xml => cmdock-l_job_0.2.0-r1.xml} | 2 +-
3 files changed, 20 insertions(+), 21 deletions(-)
diff --git a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r2.ebuild
similarity index 83%
rename from sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
rename to sci-biology/cmdock/cmdock-0.2.0-r2.ebuild
index f46747447..55e83bffb 100644
--- a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
+++ b/sci-biology/cmdock/cmdock-0.2.0-r2.ebuild
@@ -4,7 +4,7 @@
EAPI=8
PYTHON_COMPAT=( python3_{10..12} )
-BOINC_APP_OPTIONAL="true"
+BOINC_APP_OPTIONAL=1
inherit boinc-app flag-o-matic meson optfeature python-any-r1
DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
@@ -15,14 +15,11 @@ S="${WORKDIR}/${PN}-v${PV}"
LICENSE="LGPL-3 ZLIB"
SLOT="0/${PV}"
KEYWORDS="~amd64"
-IUSE="apidoc boinc cpu_flags_x86_sse2 doc test"
+IUSE="apidoc cpu_flags_x86_sse2 doc test"
# Flaky tests
RESTRICT="test"
-RDEPEND="
- boinc? ( sci-misc/boinc-wrapper )
-"
DEPEND="
dev-cpp/eigen:3
>=dev-cpp/indicators-2.3-r1
@@ -58,6 +55,8 @@ is to attach it to SiDock@home BOINC project."
INSTALL_PREFIX="${EPREFIX}/opt/${P}"
+boinc-app_add_deps
+
python_check_deps() {
use doc || return 0
@@ -77,7 +76,7 @@ src_prepare() {
src_configure() {
# very weird directory layout
local emesonargs=(
- --prefix="${INSTALL_PREFIX}"
+ --prefix="${INSTALL_PREFIX:?}"
$(meson_use apidoc)
$(meson_use doc)
$(meson_use test tests)
@@ -90,22 +89,22 @@ src_configure() {
src_install() {
meson_src_install
- python_optimize "${D}${INSTALL_PREFIX}"/bin
+ python_optimize "${D}${INSTALL_PREFIX:?}"/bin
if use boinc; then
- doappinfo "${FILESDIR}"/app_info_${PV}.xml
- dowrapper cmdock-l
+ boinc_install_appinfo "${FILESDIR}"/app_info_0.2.0-r1.xml
+ boinc_install_wrapper cmdock-l_wrapper \
+ "${FILESDIR}"/cmdock-l_job_0.2.0-r1.xml cmdock-l_job.xml
# install cmdock executable
exeinto "$(get_project_root)"
exeopts --owner root --group boinc
- newexe "${D}${INSTALL_PREFIX}"/bin/cmdock cmdock-${PV}
+ doexe "${D}${INSTALL_PREFIX:?}"/bin/cmdock
# install a blank file
- touch "${T}"/docking_out || die
insinto "$(get_project_root)"
- insopts --owner root --group boinc
- doins "${T}"/docking_out
+ insopts -m 0644 --owner root --group boinc
+ newins - docking_out
fi
}
diff --git a/sci-biology/cmdock/files/app_info_0.2.0.xml b/sci-biology/cmdock/files/app_info_0.2.0-r1.xml
similarity index 68%
rename from sci-biology/cmdock/files/app_info_0.2.0.xml
rename to sci-biology/cmdock/files/app_info_0.2.0-r1.xml
index ad23f7890..b9eb040fb 100644
--- a/sci-biology/cmdock/files/app_info_0.2.0.xml
+++ b/sci-biology/cmdock/files/app_info_0.2.0-r1.xml
@@ -1,22 +1,22 @@
<app_info>
<app>
<name>cmdock-l</name>
- <user_friendly_name>CurieMarieDock 0.2.0 long tasks</user_friendly_name>
+ <user_friendly_name>CurieMarieDock @PV@ long tasks</user_friendly_name>
</app>
<file_info>
- <name>cmdock-l_wrapper_@PV@</name>
+ <name>cmdock-l_wrapper</name>
<sticky/>
<executable/>
</file_info>
<file_info>
- <name>cmdock-@PV@</name>
+ <name>cmdock</name>
<sticky/>
<executable/>
</file_info>
<file_info>
- <name>cmdock-l_job_@PV@.xml</name>
+ <name>cmdock-l_job.xml</name>
<sticky/>
</file_info>
<file_info>
@@ -28,16 +28,16 @@
<app_name>cmdock-l</app_name>
<version_num>100</version_num>
<file_ref>
- <file_name>cmdock-l_wrapper_@PV@</file_name>
+ <file_name>cmdock-l_wrapper</file_name>
<main_program/>
</file_ref>
<file_ref>
- <file_name>cmdock-@PV@</file_name>
+ <file_name>cmdock</file_name>
<open_name>cmdock</open_name>
<copy_file/>
</file_ref>
<file_ref>
- <file_name>cmdock-l_job_@PV@.xml</file_name>
+ <file_name>cmdock-l_job.xml</file_name>
<open_name>job.xml</open_name>
<copy_file/>
</file_ref>
diff --git a/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml b/sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml
similarity index 77%
rename from sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml
rename to sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml
index a163eb29c..6d626fb82 100644
--- a/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml
+++ b/sci-biology/cmdock/files/cmdock-l_job_0.2.0-r1.xml
@@ -2,7 +2,7 @@
<task>
<application>cmdock</application>
<stdout_filename>docking_log</stdout_filename>
- <command_line>-c -j 1 -b 1 -x -r target.prm -p "@PREFIX@/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+ <command_line>-c -j 1 -b 1 -r target.prm -p "@PREFIX@/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=@PREFIX@</setenv>
^ permalink raw reply related [flat|nested] 4+ messages in thread
end of thread, other threads:[~2024-07-14 7:27 UTC | newest]
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2021-07-01 5:08 [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/files/, sci-biology/cmdock/ Anna Vyalkova
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