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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>
This commit is contained in:
Anna (cybertailor) Vyalkova
@@ -1 +1,2 @@
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DIST cmdock-v0.1.2.tar.gz 13394195 BLAKE2B bd377b6a953d1e38b527da4eda36aee7a634e9f0c400487d4092ae1939589890038fc90052d8bddb25457dd027fa929acd50e836d65bd5994af89116f4c770a7 SHA512 90d4114a10dde99d34cd7ea4b28399da744cc295adebb10f1f9771b59841cd13e07cae5218643c90dd2847cdb014867ab795649a3d1883396a3609c3344b8226
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DIST cmdock-v0.1.3.tar.gz 13416412 BLAKE2B abd6382943fb2ca2459fa493f8025e335821b96a95b88267dd493c28cd3280481b41ec6480fd3514cff126ab1077e89f075e5311393b1cd366403419e9c47454 SHA512 d941b672d14bad4fda4eaeb7aa313da1ade213241a1aee392747943a03afb6c66b3e93b8fd7eb9b1d8095b0632bd48cb062879cf445e3b54ce07069ad3087b22
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@@ -3,34 +3,31 @@
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EAPI=7
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PYTHON_COMPAT=( python3_{7..9} pypy3 )
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PYTHON_COMPAT=( python3_{7..10} pypy3 )
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DOCS_BUILDER="sphinx"
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DOCS_AUTODOC=0
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inherit python-r1 docs meson
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DOCS_DIR="docs"
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inherit python-any-r1 docs meson
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DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
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HOMEPAGE="https://gitlab.com/Jukic/cmdock"
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SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz"
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S="${WORKDIR}/${PN}-v${PV}"
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DOCS_DIR="${S}/docs"
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LICENSE="LGPL-3"
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SLOT="${PV}"
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SLOT="0/${PV}"
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KEYWORDS="~amd64"
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IUSE="boinc"
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REQUIRED_USE="doc? ( ${PYTHON_REQUIRED_USE} )"
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DEPEND="
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dev-cpp/eigen
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dev-libs/cxxopts
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boinc? ( sci-misc/boinc-wrapper )
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doc? ( ${PYTHON_DEPS} )
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"
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RDEPEND="${DEPEND}
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RDEPEND="
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dev-lang/perl
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boinc? ( sci-misc/boinc-wrapper )
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"
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BDEPEND="
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dev-cpp/eigen:3
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dev-cpp/pcg-cpp
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dev-libs/cxxopts
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"
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BDEPEND="dev-cpp/pcg-cpp"
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src_prepare() {
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default
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@@ -55,12 +52,12 @@ src_install() {
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if use boinc ; then
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insinto /var/lib/boinc/projects/www.sidock.si_sidock
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doins "${FILESDIR}/app_info.xml"
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newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml
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doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml"
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doins "${FILESDIR}/cmdock-boinc-zip_job_${PV}.xml"
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dosym "${EPREFIX}"/usr/bin/boinc-wrapper "/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}"
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dosym "${EPREFIX}"/usr/bin/boinc-wrapper "/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}"
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dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}
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dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}
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fi
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}
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78
sci-biology/cmdock/cmdock-0.1.3.ebuild
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78
sci-biology/cmdock/cmdock-0.1.3.ebuild
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@@ -0,0 +1,78 @@
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# Copyright 2021 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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PYTHON_COMPAT=( python3_{7..10} pypy3 )
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DOCS_BUILDER="sphinx"
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DOCS_AUTODOC=0
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DOCS_DIR="docs"
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inherit python-any-r1 docs meson
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DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
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HOMEPAGE="https://gitlab.com/Jukic/cmdock"
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SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz"
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S="${WORKDIR}/${PN}-v${PV}"
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LICENSE="LGPL-3"
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SLOT="0/${PV}"
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KEYWORDS="~amd64"
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IUSE="boinc"
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RDEPEND="
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dev-lang/perl
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boinc? ( sci-misc/boinc-wrapper )
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"
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BDEPEND="
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dev-cpp/eigen:3
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dev-cpp/indicators
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dev-cpp/pcg-cpp
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dev-libs/cxxopts
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"
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src_prepare() {
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default
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rm -r include/indicators || die
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sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep = declare_dependency(include_directories: '/usr/include')|" -i meson.build || die
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}
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src_configure() {
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# very weird directory layout
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local emesonargs=(
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--prefix="${EPREFIX}/opt/cmdock-${PV}"
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)
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meson_src_configure
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}
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src_compile() {
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meson_src_compile
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docs_compile
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}
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src_install() {
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meson_src_install
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if use boinc ; then
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insinto /var/lib/boinc/projects/www.sidock.si_sidock
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newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml
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doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml"
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doins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml"
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newins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml" cmdock-boinc-zip_job_${PV}.xml
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dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}
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dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV}
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dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}
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fi
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}
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pkg_postinst() {
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if use boinc ; then
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touch /var/lib/boinc/projects/www.sidock.si_sidock/docking_out.sd || die
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elog
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elog "The easiest way to do something useful with this application"
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elog "is to attach it to SiDock@home BOINC project."
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elog
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elog "- Master URL: https://sidock.si/sidock/"
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elog "- Invitation code: Crunch_4Science"
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fi
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}
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@@ -47,7 +47,7 @@
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</app_version>
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<app_version>
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<app_name>cmdock-boinc-zip</app_name>
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<version_num>200</version_num>
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<version_num>204</version_num>
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<file_ref>
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<file_name>cmdock-boinc-zip_wrapper_0.1.2</file_name>
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<main_program/>
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95
sci-biology/cmdock/files/app_info_0.1.3.xml
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95
sci-biology/cmdock/files/app_info_0.1.3.xml
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@@ -0,0 +1,95 @@
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<app_info>
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<app>
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<name>cmdock-boinc</name>
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<user_friendly_name>CurieMarieDock on BOINC</user_friendly_name>
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</app>
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<app>
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<name>cmdock-boinc-zip</name>
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<user_friendly_name>CurieMarieDock on BOINC + zipped input</user_friendly_name>
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</app>
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<app>
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<name>cmdock-boinc-zcp</name>
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<user_friendly_name>CurieMarieDock on BOINC + zipped input, checkpoints and progress bar</user_friendly_name>
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</app>
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<file_info>
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<name>cmdock-wrapper_0.1.3</name>
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<executable/>
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</file_info>
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<file_info>
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<name>cmdock-boinc-zcp_wrapper_0.1.3</name>
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<executable/>
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</file_info>
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<file_info>
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<name>cmdock-boinc-zip_wrapper_0.1.3</name>
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<executable/>
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</file_info>
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<file_info>
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<name>cmdock-boinc_job_0.1.3.xml</name>
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</file_info>
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<file_info>
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<name>cmdock-boinc-zcp_job_0.1.3.xml</name>
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</file_info>
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<file_info>
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<name>cmdock-boinc-zip_job_0.1.3.xml</name>
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</file_info>
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<file_info>
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<name>docking_out.sd</name>
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</file_info>
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<app_version>
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<app_name>cmdock-boinc</app_name>
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<version_num>103</version_num>
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<file_ref>
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<file_name>cmdock-wrapper_0.1.3</file_name>
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<main_program/>
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</file_ref>
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<file_ref>
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<file_name>cmdock-boinc_job_0.1.3.xml</file_name>
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<open_name>job.xml</open_name>
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<copy_file/>
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</file_ref>
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<file_ref>
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<file_name>docking_out.sd</file_name>
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<open_name>docking_out.sd</open_name>
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<copy_file/>
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</file_ref>
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</app_version>
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<app_version>
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<app_name>cmdock-boinc-zcp</app_name>
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<version_num>100</version_num>
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<file_ref>
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<file_name>cmdock-boinc-zcp_wrapper_0.1.3</file_name>
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<main_program/>
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</file_ref>
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<file_ref>
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<file_name>cmdock-boinc-zcp_job_0.1.3.xml</file_name>
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<open_name>job.xml</open_name>
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<copy_file/>
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</file_ref>
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<file_ref>
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<file_name>docking_out.sd</file_name>
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<open_name>docking_out.sd</open_name>
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<copy_file/>
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</file_ref>
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</app_version>
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<app_version>
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<app_name>cmdock-boinc-zip</app_name>
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<version_num>300</version_num>
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<file_ref>
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<file_name>cmdock-boinc-zip_wrapper_0.1.3</file_name>
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<main_program/>
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</file_ref>
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<file_ref>
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<file_name>cmdock-boinc-zip_job_0.1.3.xml</file_name>
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<open_name>job.xml</open_name>
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<copy_file/>
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</file_ref>
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<file_ref>
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<file_name>docking_out.sd</file_name>
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<open_name>docking_out.sd</open_name>
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<copy_file/>
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</file_ref>
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</app_version>
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</app_info>
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15
sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
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15
sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
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@@ -0,0 +1,15 @@
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<job_desc>
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<task>
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<application>/opt/cmdock-0.1.3/build/cmdock</application>
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<stdout_filename>docking_log</stdout_filename>
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<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>
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<checkpoint_filename>docking_out.chk</checkpoint_filename>
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<fraction_done_filename>docking_out.progress</fraction_done_filename>
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<setenv>CMDOCK_ROOT=/opt/cmdock-0.1.3</setenv>
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<setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv>
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<setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv>
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</task>
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<unzip_input>
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<zipfilename>ligands.zip</zipfilename>
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</unzip_input>
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</job_desc>
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@@ -2,7 +2,8 @@
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<task>
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<application>/opt/cmdock-0.1.2/build/cmdock</application>
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<stdout_filename>docking_log</stdout_filename>
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<command_line>-r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
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<command_line>-c -r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
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<checkpoint_filename>docking_out.chk</checkpoint_filename>
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<setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv>
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<setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH</setenv>
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<setenv>PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB</setenv>
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10
sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
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10
sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
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@@ -0,0 +1,10 @@
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<job_desc>
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<task>
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<application>/opt/cmdock-0.1.3/build/cmdock</application>
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<stdout_filename>docking_log</stdout_filename>
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<command_line>-r target.prm -p /opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
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<setenv>CMDOCK_ROOT=/opt/cmdock-0.1.3</setenv>
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<setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv>
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<setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv>
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</task>
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</job_desc>
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