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sci-biology/cmdock: drop obsolete

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Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
This commit is contained in:
Anna (cybertailor) Vyalkova
2021-06-27 13:51:43 +05:00
parent 5a78ed8726
commit eb972dae49
8 changed files with 4 additions and 242 deletions
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1
sci-biology/cmdock/Manifest
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@@ -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

74
sci-biology/cmdock/cmdock-0.1.2.ebuild
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@@ -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
}

13
sci-biology/cmdock/cmdock-0.1.3.ebuild
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@@ -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
}

66
sci-biology/cmdock/files/app_info_0.1.2.xml
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@@ -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>

58
sci-biology/cmdock/files/app_info_0.1.3.xml
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@@ -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>

14
sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
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@@ -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>

10
sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
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@@ -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>

10
sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
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@@ -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>