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author | 2021-05-29 18:37:10 +0500 | |
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committer | 2021-05-29 20:48:30 +0500 | |
commit | aba20d3142c80878bbc1a3b045f14c849a63cb63 (patch) | |
tree | 38793e78e1de5e9a041f3f483a68e93bb6f34b4f /sci-biology | |
parent | dev-cpp/indicators: initial import (diff) | |
download | guru-aba20d3142c80878bbc1a3b045f14c849a63cb63.tar.gz guru-aba20d3142c80878bbc1a3b045f14c849a63cb63.tar.bz2 guru-aba20d3142c80878bbc1a3b045f14c849a63cb63.zip |
sci-biology/cmdock: add 0.1.3
* revise deps
* fix symlinks
* replace slotting with subslotting
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/cmdock/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/cmdock/cmdock-0.1.2.ebuild | 29 | ||||
-rw-r--r-- | sci-biology/cmdock/cmdock-0.1.3.ebuild | 78 | ||||
-rw-r--r-- | sci-biology/cmdock/files/app_info_0.1.2.xml (renamed from sci-biology/cmdock/files/app_info.xml) | 2 | ||||
-rw-r--r-- | sci-biology/cmdock/files/app_info_0.1.3.xml | 95 | ||||
-rw-r--r-- | sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml | 15 | ||||
-rw-r--r-- | sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 3 | ||||
-rw-r--r-- | sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml | 10 |
8 files changed, 215 insertions, 18 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_${PV} fi } diff --git a/sci-biology/cmdock/cmdock-0.1.3.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild new file mode 100644 index 000000000..c4a2da7b4 --- /dev/null +++ b/sci-biology/cmdock/cmdock-0.1.3.ebuild @@ -0,0 +1,78 @@ +# Copyright 2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{7..10} pypy3 ) +DOCS_BUILDER="sphinx" +DOCS_AUTODOC=0 +DOCS_DIR="docs" +inherit python-any-r1 docs meson + +DESCRIPTION="Program for docking ligands to proteins and nucleic acids" +HOMEPAGE="https://gitlab.com/Jukic/cmdock" +SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz" +S="${WORKDIR}/${PN}-v${PV}" + +LICENSE="LGPL-3" +SLOT="0/${PV}" +KEYWORDS="~amd64" +IUSE="boinc" + +RDEPEND=" + dev-lang/perl + boinc? ( sci-misc/boinc-wrapper ) +" +BDEPEND=" + dev-cpp/eigen:3 + dev-cpp/indicators + dev-cpp/pcg-cpp + dev-libs/cxxopts +" + +src_prepare() { + default + rm -r include/indicators || die + sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep = declare_dependency(include_directories: '/usr/include')|" -i meson.build || die +} + +src_configure() { + # very weird directory layout + local emesonargs=( + --prefix="${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-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} + 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_info.xml b/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> |