From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 52C9013835A for ; Sat, 29 May 2021 15:49:24 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 7276DE0866; Sat, 29 May 2021 15:49:23 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 496F0E0866 for ; Sat, 29 May 2021 15:49:23 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 07239340F15 for ; Sat, 29 May 2021 15:49:22 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 5BE4A793 for ; Sat, 29 May 2021 15:49:20 +0000 (UTC) From: "Anna Vyalkova" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Anna Vyalkova" Message-ID: <1622303310.aba20d3142c80878bbc1a3b045f14c849a63cb63.cybertailor@gentoo> Subject: [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/ X-VCS-Repository: repo/proj/guru X-VCS-Files: sci-biology/cmdock/Manifest sci-biology/cmdock/cmdock-0.1.2.ebuild sci-biology/cmdock/cmdock-0.1.3.ebuild sci-biology/cmdock/files/app_info.xml sci-biology/cmdock/files/app_info_0.1.2.xml sci-biology/cmdock/files/app_info_0.1.3.xml sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml X-VCS-Directories: sci-biology/cmdock/ sci-biology/cmdock/files/ X-VCS-Committer: cybertailor X-VCS-Committer-Name: Anna Vyalkova X-VCS-Revision: aba20d3142c80878bbc1a3b045f14c849a63cb63 X-VCS-Branch: dev Date: Sat, 29 May 2021 15:49:20 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 626c98a1-79d4-430b-998c-a8b79625a86b X-Archives-Hash: 5bdac0df1bddad8919fde3f7a74e83d5 commit: aba20d3142c80878bbc1a3b045f14c849a63cb63 Author: Anna (cybertailor) Vyalkova sysrq in> AuthorDate: Sat May 29 13:37:10 2021 +0000 Commit: Anna Vyalkova sysrq in> CommitDate: Sat May 29 15:48:30 2021 +0000 URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=aba20d31 sci-biology/cmdock: add 0.1.3 * revise deps * fix symlinks * replace slotting with subslotting Signed-off-by: Anna (cybertailor) Vyalkova sysrq.in> sci-biology/cmdock/Manifest | 1 + sci-biology/cmdock/cmdock-0.1.2.ebuild | 29 +++---- .../{cmdock-0.1.2.ebuild => cmdock-0.1.3.ebuild} | 35 ++++---- .../files/{app_info.xml => app_info_0.1.2.xml} | 2 +- sci-biology/cmdock/files/app_info_0.1.3.xml | 95 ++++++++++++++++++++++ .../cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml | 15 ++++ .../cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 3 +- .../cmdock/files/cmdock-boinc_job_0.1.3.xml | 10 +++ 8 files changed, 155 insertions(+), 35 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_${PV} fi } diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild similarity index 64% copy from sci-biology/cmdock/cmdock-0.1.2.ebuild copy to sci-biology/cmdock/cmdock-0.1.3.ebuild index aa5a4546b..c4a2da7b4 100644 --- a/sci-biology/cmdock/cmdock-0.1.2.ebuild +++ b/sci-biology/cmdock/cmdock-0.1.3.ebuild @@ -3,37 +3,36 @@ EAPI=7 -PYTHON_COMPAT=( python3_{7..9} pypy3 ) +PYTHON_COMPAT=( python3_{7..10} pypy3 ) DOCS_BUILDER="sphinx" DOCS_AUTODOC=0 -inherit python-r1 docs meson +DOCS_DIR="docs" +inherit python-any-r1 docs meson DESCRIPTION="Program for docking ligands to proteins and nucleic acids" HOMEPAGE="https://gitlab.com/Jukic/cmdock" SRC_URI="https://gitlab.com/Jukic/${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/indicators + dev-cpp/pcg-cpp + dev-libs/cxxopts " -BDEPEND="dev-cpp/pcg-cpp" 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 } @@ -55,12 +54,14 @@ 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_${PV}.xml" + doins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml" + newins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml" cmdock-boinc-zip_job_${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_${PV} + dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${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/files/app_info.xml b/sci-biology/cmdock/files/app_info_0.1.2.xml similarity index 97% rename from sci-biology/cmdock/files/app_info.xml rename to 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 @@ cmdock-boinc-zip - 200 + 204 cmdock-boinc-zip_wrapper_0.1.2 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 @@ + + + cmdock-boinc + CurieMarieDock on BOINC + + + cmdock-boinc-zip + CurieMarieDock on BOINC + zipped input + + + cmdock-boinc-zcp + CurieMarieDock on BOINC + zipped input, checkpoints and progress bar + + + + cmdock-wrapper_0.1.3 + + + + cmdock-boinc-zcp_wrapper_0.1.3 + + + + cmdock-boinc-zip_wrapper_0.1.3 + + + + + cmdock-boinc_job_0.1.3.xml + + + cmdock-boinc-zcp_job_0.1.3.xml + + + cmdock-boinc-zip_job_0.1.3.xml + + + docking_out.sd + + + + cmdock-boinc + 103 + + cmdock-wrapper_0.1.3 + + + + cmdock-boinc_job_0.1.3.xml + job.xml + + + + docking_out.sd + docking_out.sd + + + + + cmdock-boinc-zcp + 100 + + cmdock-boinc-zcp_wrapper_0.1.3 + + + + cmdock-boinc-zcp_job_0.1.3.xml + job.xml + + + + docking_out.sd + docking_out.sd + + + + + cmdock-boinc-zip + 300 + + cmdock-boinc-zip_wrapper_0.1.3 + + + + cmdock-boinc-zip_job_0.1.3.xml + job.xml + + + + docking_out.sd + docking_out.sd + + + + 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 @@ + + + /opt/cmdock-0.1.3/build/cmdock + docking_log + -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 + docking_out.chk + docking_out.progress + CMDOCK_ROOT=/opt/cmdock-0.1.3 + LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH + PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB + + + ligands.zip + + diff --git a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml index 2691d09ea..a11f1fe9b 100644 --- a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml +++ b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml @@ -2,7 +2,8 @@ /opt/cmdock-0.1.2/build/cmdock docking_log - -r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out + -c -r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out + docking_out.chk CMDOCK_ROOT=/opt/cmdock-0.1.2 LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml new file mode 100644 index 000000000..6082dc8fe --- /dev/null +++ b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml @@ -0,0 +1,10 @@ + + + /opt/cmdock-0.1.3/build/cmdock + docking_log + -r target.prm -p /opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out + CMDOCK_ROOT=/opt/cmdock-0.1.3 + LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH + PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB + +