sci-biology/cmdock: add 0.2.0

Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>

4 files changed, 178 insertions, 0 deletions

diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
index 5f5d12c7f..8757cee0d 100644
--- a/sci-biology/cmdock/Manifest
+++ b/sci-biology/cmdock/Manifest
@@ -1 +1,2 @@
 DIST cmdock-v0.1.4.tar.bz2 14095825 BLAKE2B 80d5d86dc11e842689255d2b673545436404fb92815bb33b5ff15eba0cd3e8970a750dfeb657d018ef31024a2ecf591bcb5c6c1f427be1d0c86a0cfc017c8aa0 SHA512 d0d9a96ef0fad8cd4b320a2339a1889e481a825c5712259e04c9e91b34de597def3100c3c9f71fa63f3eef43892a17c0114d4cc93e99424bcdcc1fc97c25f51e
+DIST cmdock-v0.2.0.tar.bz2 14155812 BLAKE2B daf2f1ac137761bf24b2295dd025e81b29eefae23b5b33c7319f87cf6ea938bcb2ce619229d84dd2af9f31785b63bab4dda95bba3e7cd4de122f94f953913694 SHA512 67eda7e712650641219d7d4d4f9c455923bc6241aa687c5b3f489e251b9e838c3bcdcc7184540ab28f96ab8f573320599669e4b52989ce33a015bceec89717c5
diff --git a/sci-biology/cmdock/cmdock-0.2.0.ebuild b/sci-biology/cmdock/cmdock-0.2.0.ebuild
new file mode 100644
index 000000000..9a91c85df
--- /dev/null
+++ b/sci-biology/cmdock/cmdock-0.2.0.ebuild
@@ -0,0 +1,112 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+BOINC_APP_OPTIONAL="true"
+inherit boinc-app flag-o-matic meson optfeature python-any-r1
+
+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.bz2"
+S="${WORKDIR}/${PN}-v${PV}"
+
+LICENSE="LGPL-3 ZLIB"
+SLOT="0/${PV}"
+KEYWORDS="~amd64"
+IUSE="apidoc boinc cpu_flags_x86_sse2 doc test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	boinc? ( sci-misc/boinc-wrapper )
+"
+DEPEND="
+	dev-cpp/eigen:3
+	dev-cpp/indicators
+	>=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
+	dev-libs/cxxopts
+"
+BDEPEND="
+	apidoc? (
+		app-doc/doxygen
+		dev-texlive/texlive-fontutils
+	)
+	doc? (
+		$(python_gen_any_dep '
+			dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]
+			dev-python/sphinx[${PYTHON_USEDEP}]
+		')
+	)
+	test? ( ${PYTHON_DEPS} )
+"
+
+DOCS=( README.md changelog.md )
+
+BOINC_MASTER_URL="https://www.sidock.si/sidock/"
+BOINC_INVITATION_CODE="Crunch_4Science"
+BOINC_APP_HELPTEXT=\
+"The easiest way to do something useful with this application
+is to attach it to SiDock@home BOINC project."
+
+INSTALL_PREFIX="${EPREFIX}/opt/${P}"
+
+python_check_deps() {
+	use doc || return 0
+
+	python_has_version "dev-python/sphinx[${PYTHON_USEDEP}]" &&
+	python_has_version "dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]"
+}
+
+foreach_wrapper_job() {
+	sed -e "s:@PREFIX@:${INSTALL_PREFIX}:g" -i "${1}" || die
+}
+
+src_prepare() {
+	default
+	python_fix_shebang "${S}"/bin
+}
+
+src_configure() {
+	# very weird directory layout
+	local emesonargs=(
+		--prefix="${INSTALL_PREFIX}"
+		$(meson_use apidoc)
+		$(meson_use doc)
+		$(meson_use test tests)
+		-Ddocdir="${EPREFIX}"/usr/share/doc/${PF}
+	)
+	meson_src_configure
+
+	use cpu_flags_x86_sse2 || append-cppflags "-DBUNDLE_NO_SSE"
+}
+
+src_install() {
+	meson_src_install
+	python_optimize "${D}${INSTALL_PREFIX}"/bin
+
+	if use boinc; then
+		doappinfo "${FILESDIR}"/app_info_${PV}.xml
+		dowrapper cmdock-l
+
+		# install cmdock executable
+		exeinto "$(get_project_root)"
+		exeopts --owner root --group boinc
+		newexe "${D}${INSTALL_PREFIX}"/bin/cmdock cmdock-${PV}
+
+		# install a blank file
+		touch "${T}"/docking_out || die
+		insinto "$(get_project_root)"
+		insopts --owner root --group boinc
+		doins "${T}"/docking_out
+	fi
+}
+
+pkg_postinst() {
+	optfeature "sdtether.py and sdrmsd.py scripts" "dev-python/numpy sci-chemistry/openbabel[python]"
+	use boinc && boinc-app_pkg_postinst
+}
+
+pkg_postrm() {
+	use boinc && boinc-app_pkg_postrm
+}
diff --git a/sci-biology/cmdock/files/app_info_0.2.0.xml b/sci-biology/cmdock/files/app_info_0.2.0.xml
new file mode 100644
index 000000000..ad23f7890
--- /dev/null
+++ b/sci-biology/cmdock/files/app_info_0.2.0.xml
@@ -0,0 +1,50 @@
+<app_info>
+<app>
+	<name>cmdock-l</name>
+	<user_friendly_name>CurieMarieDock 0.2.0 long tasks</user_friendly_name>
+</app>
+
+<file_info>
+	<name>cmdock-l_wrapper_@PV@</name>
+	<sticky/>
+	<executable/>
+</file_info>
+<file_info>
+	<name>cmdock-@PV@</name>
+	<sticky/>
+	<executable/>
+</file_info>
+
+<file_info>
+	<name>cmdock-l_job_@PV@.xml</name>
+	<sticky/>
+</file_info>
+<file_info>
+	<name>docking_out</name>
+	<sticky/>
+</file_info>
+
+<app_version>
+	<app_name>cmdock-l</app_name>
+	<version_num>100</version_num>
+	<file_ref>
+		<file_name>cmdock-l_wrapper_@PV@</file_name>
+		<main_program/>
+	</file_ref>
+	<file_ref>
+		<file_name>cmdock-@PV@</file_name>
+		<open_name>cmdock</open_name>
+		<copy_file/>
+	</file_ref>
+	<file_ref>
+		<file_name>cmdock-l_job_@PV@.xml</file_name>
+		<open_name>job.xml</open_name>
+		<copy_file/>
+	</file_ref>
+	<file_ref>
+		<file_name>docking_out</file_name>
+		<open_name>docking_out</open_name>
+		<copy_file/>
+	</file_ref>
+</app_version>
+</app_info>
diff --git a/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml b/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml
new file mode 100644
index 000000000..a163eb29c
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml
@@ -0,0 +1,15 @@
+<job_desc>
+	<task>
+		<application>cmdock</application>
+		<stdout_filename>docking_log</stdout_filename>
+		<command_line>-c -j 1 -b 1 -x -r target.prm -p "@PREFIX@/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+		<checkpoint_filename>docking_out.chk</checkpoint_filename>
+		<fraction_done_filename>docking_out.progress</fraction_done_filename>
+		<setenv>CMDOCK_ROOT=@PREFIX@</setenv>
+		<setenv>LD_LIBRARY_PATH=@PREFIX@/lib:$LD_LIBRARY_PATH</setenv>
+		<setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv>
+	</task>
+	<unzip_input>
+		<zipfilename>ligands.zip</zipfilename>
+	</unzip_input>
+</job_desc>