sci-biology/cmdock: initial import

Signed-off-by: Anna Vyalkova <cyber@sysrq.in>

6 files changed, 181 insertions, 0 deletions

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>cyber+gentoo@sysrq.in</email>
+		<name>Anna</name>
+	</maintainer>
+	<use>
+		<flag name="boinc">
+			Use CmDock with SiDock@home BOINC project
+		</flag>
+	</use>
+</pkgmetadata>