[gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/

[Anna Vyalkova]

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>cyber+gentoo@×××××.in</email>