commit: 8b0e3834b1db271f7499bfb1721eeb2d74b0907a
Author: Anna Vyalkova <cyber <AT> sysrq <DOT> in>
AuthorDate: Tue May 18 21:31:09 2021 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> 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 <cyber <AT> 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 @@
+<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>100</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>
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 @@
+<job_desc>
+ <task>
+ <application>/opt/cmdock/build/cmdock-0.1.2</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:$PERL5LIB</setenv>
+ </task>
+ <unzip_input>
+ <zipfilename>ligands.zip</zipfilename>
+ </unzip_input>
+</job_desc>
diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
new file mode 100644
index 000000000..aa3042498
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml
@@ -0,0 +1,10 @@
+<job_desc>
+ <task>
+ <application>/opt/cmdock/build/cmdock-0.1.2</application>
+ <stdout_filename>docking_log</stdout_filename>
+ <command_line>-r target.prm -p
/opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o
docking_out</command_line>
+ <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv>
+
<setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH</setenv>
+ <setenv>PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB</setenv>
+ </task>
+</job_desc>
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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
+<pkgmetadata>
+ <upstream>
+ <remote-id type="gitlab">Jukic/cmdock</remote-id>
+ <bugs-to>https://gitlab.com/Jukic/cmdock/-/issues</bugs-to>
+ </upstream>
+ <maintainer type="person">
+ <email>[email protected]</email>
+ <name>Anna</name>
+ </maintainer>
+ <use>
+ <flag name="boinc">
+ Use CmDock with SiDock@home BOINC project
+ </flag>
+ </use>
+</pkgmetadata>
