commit: 43200432ac81cfb799df3a1a62076920d42f8f5a
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Fri Jan 6 05:30:16 2023 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Sat Jan 7 09:40:44 2023 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=43200432
sci-biology/cmdock: add 0.2.0
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/Manifest | 1 +
sci-biology/cmdock/cmdock-0.2.0.ebuild | 112 ++++++++++++++++++++++++
sci-biology/cmdock/files/app_info_0.2.0.xml | 50 +++++++++++
sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml | 15 ++++
4 files changed, 178 insertions(+)
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>
