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 3F24E13835B for ; Tue, 18 May 2021 21:31:25 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 71446E076B; Tue, 18 May 2021 21:31:24 +0000 (UTC) Received: from smtp.gentoo.org (mail.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (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 4B0BDE076B for ; Tue, 18 May 2021 21:31:24 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (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 E1FE6335D47 for ; Tue, 18 May 2021 21:31:22 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 4D15B78E for ; Tue, 18 May 2021 21:31:21 +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: <1621373478.8b0e3834b1db271f7499bfb1721eeb2d74b0907a.cybertailor@gentoo> Subject: [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/files/, sci-biology/cmdock/ X-VCS-Repository: repo/proj/guru X-VCS-Files: sci-biology/cmdock/Manifest sci-biology/cmdock/cmdock-0.1.2.ebuild sci-biology/cmdock/files/app_config.xml sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml sci-biology/cmdock/metadata.xml X-VCS-Directories: sci-biology/cmdock/ sci-biology/cmdock/files/ X-VCS-Committer: cybertailor X-VCS-Committer-Name: Anna Vyalkova X-VCS-Revision: 8b0e3834b1db271f7499bfb1721eeb2d74b0907a X-VCS-Branch: dev Date: Tue, 18 May 2021 21:31:21 +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: 66aeb31e-fcb5-4545-9ce4-ef4236857b9d X-Archives-Hash: ef7c096ad22bcda72bb0c73749c61550 commit: 8b0e3834b1db271f7499bfb1721eeb2d74b0907a Author: Anna Vyalkova sysrq in> AuthorDate: Tue May 18 21:31:09 2021 +0000 Commit: Anna Vyalkova sysrq in> CommitDate: Tue May 18 21:31:18 2021 +0000 URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=8b0e3834 sci-biology/cmdock: initial import Signed-off-by: Anna Vyalkova sysrq.in> sci-biology/cmdock/Manifest | 1 + sci-biology/cmdock/cmdock-0.1.2.ebuild | 74 ++++++++++++++++++++++ sci-biology/cmdock/files/app_config.xml | 66 +++++++++++++++++++ .../cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 13 ++++ .../cmdock/files/cmdock-boinc_job_0.1.2.xml | 10 +++ sci-biology/cmdock/metadata.xml | 17 +++++ 6 files changed, 181 insertions(+) diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest new file mode 100644 index 000000000..25663d438 --- /dev/null +++ b/sci-biology/cmdock/Manifest @@ -0,0 +1 @@ +DIST cmdock-v0.1.2.tar.gz 13394195 BLAKE2B bd377b6a953d1e38b527da4eda36aee7a634e9f0c400487d4092ae1939589890038fc90052d8bddb25457dd027fa929acd50e836d65bd5994af89116f4c770a7 SHA512 90d4114a10dde99d34cd7ea4b28399da744cc295adebb10f1f9771b59841cd13e07cae5218643c90dd2847cdb014867ab795649a3d1883396a3609c3344b8226 diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild b/sci-biology/cmdock/cmdock-0.1.2.ebuild new file mode 100644 index 000000000..34c37a5ee --- /dev/null +++ b/sci-biology/cmdock/cmdock-0.1.2.ebuild @@ -0,0 +1,74 @@ +# Copyright 2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{7..9} pypy3 ) +DOCS_BUILDER="sphinx" +DOCS_AUTODOC=0 +inherit python-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="${PV}" +KEYWORDS="~amd64" +IUSE="boinc" + +DEPEND=" + dev-cpp/eigen + dev-libs/cxxopts + boinc? ( sci-misc/boinc-wrapper ) +" +RDEPEND="${DEPEND} + dev-lang/perl +" +BDEPEND="dev-cpp/pcg-cpp" + +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 + doins "${FILESDIR}/app_config.xml" + doins "${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_${PV}" + fi +} + +pkg_postinst() { + if use boinc ; then + touch /var/lib/boinc/projects/www.sidock.si_sidock/docking_out.sd || die + elog + elog "The easiest way to do something useful with this application" + elog "is to attach it to SiDock@home BOINC project." + elog + elog "- Master URL: https://sidock.si/sidock/" + elog "- Invitation code: Crunch_4Science" + fi +} diff --git a/sci-biology/cmdock/files/app_config.xml b/sci-biology/cmdock/files/app_config.xml new file mode 100644 index 000000000..6a41b0bb2 --- /dev/null +++ b/sci-biology/cmdock/files/app_config.xml @@ -0,0 +1,66 @@ + + + cmdock-boinc + CurieMarieDock on BOINC + + + cmdock-boinc-zip + CurieMarieDock on BOINC + zipped input + + + + cmdock-wrapper_0.1.2 + + + + cmdock-boinc-zip_wrapper_0.1.2 + + + + + cmdock-boinc_job_0.1.2.xml + + + cmdock-boinc-zip_job_0.1.2.xml + + + docking_out.sd + + + + cmdock-boinc + 102 + + cmdock-wrapper_0.1.2 + + + + cmdock-boinc_job_0.1.2.xml + job.xml + + + + docking_out.sd + docking_out.sd + + + + + cmdock-boinc-zip + 100 + + cmdock-boinc-zip_wrapper_0.1.2 + + + + cmdock-boinc-zip_job_0.1.2.xml + job.xml + + + + docking_out.sd + docking_out.sd + + + + diff --git a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml new file mode 100644 index 000000000..3b89cdfd2 --- /dev/null +++ b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml @@ -0,0 +1,13 @@ + + + /opt/cmdock/build/cmdock-0.1.2 + docking_log + -r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out + CMDOCK_ROOT=/opt/cmdock-0.1.2 + LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH + PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB + + + ligands.zip + + diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml new file mode 100644 index 000000000..aa3042498 --- /dev/null +++ b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml @@ -0,0 +1,10 @@ + + + /opt/cmdock/build/cmdock-0.1.2 + docking_log + -r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out + CMDOCK_ROOT=/opt/cmdock-0.1.2 + LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH + PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB + + diff --git a/sci-biology/cmdock/metadata.xml b/sci-biology/cmdock/metadata.xml new file mode 100644 index 000000000..9bb734387 --- /dev/null +++ b/sci-biology/cmdock/metadata.xml @@ -0,0 +1,17 @@ + + + + + Jukic/cmdock + https://gitlab.com/Jukic/cmdock/-/issues + + + cyber+gentoo@sysrq.in + Anna + + + + Use CmDock with SiDock@home BOINC project + + +