commit: 4d7271caedd3ec77361bba7d98772767dfee8b78 Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in> AuthorDate: Mon Jul 19 10:55:37 2021 +0000 Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in> CommitDate: Thu Jul 22 08:27:39 2021 +0000 URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=4d7271ca
sci-biology/cmdock: make it prettier, fix perms Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in> sci-biology/cmdock/cmdock-0.1.3.ebuild | 31 +++++++++++++++++----- .../cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml | 10 +++---- sci-biology/cmdock/metadata.xml | 1 + 3 files changed, 30 insertions(+), 12 deletions(-) diff --git a/sci-biology/cmdock/cmdock-0.1.3.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild index e42b1f253..13e4bc2cc 100644 --- a/sci-biology/cmdock/cmdock-0.1.3.ebuild +++ b/sci-biology/cmdock/cmdock-0.1.3.ebuild @@ -10,7 +10,7 @@ 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"; +HOMEPAGE="https://gitlab.com/Jukic/cmdock https://www.rxdock.org"; SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz"; S="${WORKDIR}/${PN}-v${PV}" @@ -30,6 +30,8 @@ BDEPEND=" dev-libs/cxxopts " +MY_PREFIX="${EPREFIX}/opt/${P}" + src_prepare() { default rm -r include/indicators || die @@ -38,7 +40,7 @@ src_prepare() { src_configure() { # very weird directory layout local emesonargs=( - --prefix="${EPREFIX}/opt/cmdock-${PV}" + --prefix="${MY_PREFIX}" ) meson_src_configure } @@ -52,17 +54,32 @@ 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 "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml" + local project_root="/var/lib/boinc/projects/www.sidock.si_sidock" + + local wrappers=( ${PN}-boinc-zcp ) + + insinto ${project_root} + insopts --owner boinc --group boinc + + newins "${FILESDIR}"/app_info_${PV}.xml app_info.xml + touch "${ED}${project_root}"/docking_out.sd || die + fowners boinc:boinc ${project_root}/docking_out.sd + + for app in "${wrappers[@]}" ; do + wrapperjob="${app}_job_${PV}.xml" + wrapperexe="${app}_wrapper_${PV}" + + dosym -r /usr/bin/boinc-wrapper "${project_root}/${wrapperexe}" - dosym -r /usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV} + cp "${FILESDIR}"/${wrapperjob} "${S}" || die + sed "s:@PREFIX@:${MY_PREFIX}:g" -i ${wrapperjob} || die + doins ${wrapperjob} + done fi } pkg_postinst() { if use boinc ; then - touch /var/lib/boinc/projects/www.sidock.si_sidock/docking_out.sd || die elog elog "The easiest way to do something useful with this application" elog "is to attach it to SiDock@home BOINC project." diff --git a/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml index 3c7818151..074bb29d4 100644 --- a/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml +++ b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml @@ -1,13 +1,13 @@ <job_desc> <task> - <application>/opt/cmdock-0.1.3/build/cmdock</application> + <application>@PREFIX@/build/cmdock</application> <stdout_filename>docking_log</stdout_filename> - <command_line>-c -j 1 -r target.prm -p /opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line> + <command_line>-c -j 1 -r target.prm -p @PREFIX@/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line> <checkpoint_filename>docking_out.chk</checkpoint_filename> <fraction_done_filename>docking_out.progress</fraction_done_filename> - <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.3</setenv> - <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv> - <setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv> + <setenv>CMDOCK_ROOT=@PREFIX@</setenv> + <setenv>LD_LIBRARY_PATH=@PREFIX@/build:$LD_LIBRARY_PATH</setenv> + <setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv> </task> <unzip_input> <zipfilename>ligands.zip</zipfilename> diff --git a/sci-biology/cmdock/metadata.xml b/sci-biology/cmdock/metadata.xml index 9bb734387..f0cb44b3d 100644 --- a/sci-biology/cmdock/metadata.xml +++ b/sci-biology/cmdock/metadata.xml @@ -4,6 +4,7 @@ <upstream> <remote-id type="gitlab">Jukic/cmdock</remote-id> <bugs-to>https://gitlab.com/Jukic/cmdock/-/issues</bugs-to> + <doc>https://www.rxdock.org/api-documentation/devel/html</doc> </upstream> <maintainer type="person"> <email>[email protected]</email>
