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author | Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in> | 2023-01-06 10:30:16 +0500 |
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committer | Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in> | 2023-01-07 14:40:44 +0500 |
commit | 43200432ac81cfb799df3a1a62076920d42f8f5a (patch) | |
tree | c21a9cb3b72f412f87022de11023a4f5ea5d2aa4 /sci-biology | |
parent | sys-boot/zfsbootmenu: Add upstream to metadata.xml for sys-boot/zfsbootmenu (diff) | |
download | guru-43200432ac81cfb799df3a1a62076920d42f8f5a.tar.gz guru-43200432ac81cfb799df3a1a62076920d42f8f5a.tar.bz2 guru-43200432ac81cfb799df3a1a62076920d42f8f5a.zip |
sci-biology/cmdock: add 0.2.0
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/cmdock/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/cmdock/cmdock-0.2.0.ebuild | 112 | ||||
-rw-r--r-- | sci-biology/cmdock/files/app_info_0.2.0.xml | 50 | ||||
-rw-r--r-- | sci-biology/cmdock/files/cmdock-l_job_0.2.0.xml | 15 |
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> |