diff options
| -rw-r--r-- | sci-biology/cmdock/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/cmdock/cmdock-0.1.3.ebuild | 90 | ||||
| -rw-r--r-- | sci-biology/cmdock/cmdock-0.1.4.ebuild | 94 | ||||
| -rw-r--r-- | sci-biology/cmdock/files/app_info_0.1.4.xml | 37 | ||||
| -rw-r--r-- | sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml | 15 |
5 files changed, 147 insertions, 90 deletions
diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest index 84968a8f8..cac8acdf0 100644 --- a/sci-biology/cmdock/Manifest +++ b/sci-biology/cmdock/Manifest @@ -1 +1,2 @@ DIST cmdock-v0.1.3.tar.gz 13416412 BLAKE2B abd6382943fb2ca2459fa493f8025e335821b96a95b88267dd493c28cd3280481b41ec6480fd3514cff126ab1077e89f075e5311393b1cd366403419e9c47454 SHA512 d941b672d14bad4fda4eaeb7aa313da1ade213241a1aee392747943a03afb6c66b3e93b8fd7eb9b1d8095b0632bd48cb062879cf445e3b54ce07069ad3087b22 +DIST cmdock-v0.1.4.tar.gz 14487352 BLAKE2B 3f212d596a12046f9a3b04376ca3e6d67f4391edba6f9c6e1fd372e7c7dbb23727ebd77787f125e57afca16e0cffc9b734dcdc7a83a825c52737218df371cbfd SHA512 6e1a366d82b311da0fdcd99ecf3e10962073453c7fdec9142854d472336f7f918bb76368b52e5904bf30e0aea6b8476a3ab522469daeaef52293ac481741b4bb diff --git a/sci-biology/cmdock/cmdock-0.1.3.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild deleted file mode 100644 index 13e4bc2cc..000000000 --- a/sci-biology/cmdock/cmdock-0.1.3.ebuild +++ /dev/null @@ -1,90 +0,0 @@ -# Copyright 2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} pypy3 ) -DOCS_BUILDER="sphinx" -DOCS_AUTODOC=0 -DOCS_DIR="docs" -inherit python-any-r1 docs meson - -DESCRIPTION="Program for docking ligands to proteins and nucleic acids" -HOMEPAGE="https://gitlab.com/Jukic/cmdock https://www.rxdock.org" -SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz" -S="${WORKDIR}/${PN}-v${PV}" - -LICENSE="LGPL-3" -SLOT="0/${PV}" -KEYWORDS="~amd64" -IUSE="boinc" - -RDEPEND=" - dev-lang/perl - boinc? ( sci-misc/boinc-wrapper ) -" -BDEPEND=" - dev-cpp/eigen:3 - dev-cpp/indicators - >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1 - dev-libs/cxxopts -" - -MY_PREFIX="${EPREFIX}/opt/${P}" - -src_prepare() { - default - rm -r include/indicators || die -} - -src_configure() { - # very weird directory layout - local emesonargs=( - --prefix="${MY_PREFIX}" - ) - meson_src_configure -} - -src_compile() { - meson_src_compile - docs_compile -} - -src_install() { - meson_src_install - - if use boinc ; then - local project_root="/var/lib/boinc/projects/www.sidock.si_sidock" - - local wrappers=( ${PN}-boinc-zcp ) - - insinto ${project_root} - insopts --owner boinc --group boinc - - newins "${FILESDIR}"/app_info_${PV}.xml app_info.xml - touch "${ED}${project_root}"/docking_out.sd || die - fowners boinc:boinc ${project_root}/docking_out.sd - - for app in "${wrappers[@]}" ; do - wrapperjob="${app}_job_${PV}.xml" - wrapperexe="${app}_wrapper_${PV}" - - dosym -r /usr/bin/boinc-wrapper "${project_root}/${wrapperexe}" - - cp "${FILESDIR}"/${wrapperjob} "${S}" || die - sed "s:@PREFIX@:${MY_PREFIX}:g" -i ${wrapperjob} || die - doins ${wrapperjob} - done - fi -} - -pkg_postinst() { - if use boinc ; then - elog - elog "The easiest way to do something useful with this application" - elog "is to attach it to SiDock@home BOINC project." - elog - elog "- Master URL: https://sidock.si/sidock/" - elog "- Invitation code: Crunch_4Science" - fi -} diff --git a/sci-biology/cmdock/cmdock-0.1.4.ebuild b/sci-biology/cmdock/cmdock-0.1.4.ebuild new file mode 100644 index 000000000..70befcfcc --- /dev/null +++ b/sci-biology/cmdock/cmdock-0.1.4.ebuild @@ -0,0 +1,94 @@ +# Copyright 2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{8..10} pypy3 ) + +BOINC_APP_OPTIONAL="true" + +DOCS_BUILDER="sphinx" +DOCS_AUTODOC=0 +DOCS_DIR="docs" + +inherit python-any-r1 boinc-app docs flag-o-matic meson + +DESCRIPTION="Program for docking ligands to proteins and nucleic acids" +HOMEPAGE="https://gitlab.com/Jukic/cmdock https://www.rxdock.org" +SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz" +S="${WORKDIR}/${PN}-v${PV}" + +LICENSE="LGPL-3 ZLIB" +SLOT="0/${PV}" +KEYWORDS="~amd64" +IUSE="apidoc boinc cpu_flags_x86_sse2" + +RDEPEND=" + dev-lang/perl + boinc? ( sci-misc/boinc-wrapper ) +" +BDEPEND=" + dev-cpp/eigen:3 + dev-cpp/indicators + >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1 + dev-libs/cxxopts + doc? ( app-doc/doxygen ) +" + +DOCS=( INSTALL.md README.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." + +foreach_wrapper_job() { + sed -i "$1" \ + -e "s:@PREFIX@:${EPREFIX}/opt/${P}:g" || die +} + +src_configure() { + # very weird directory layout + local emesonargs=( + --prefix="${EPREFIX}/opt/${P}" + ) + meson_src_configure + + use cpu_flags_x86_sse2 || append-cppflags "-DBUNDLE_NO_SSE" +} + +src_compile() { + meson_src_compile + + # subshell prevents overriding global + # DOCS_BUILDER and DOCS_OUTDIR + ( + DOCS_BUILDER="doxygen" + DOCS_OUTDIR="${S}/_build/html/api" + docs_compile + ) + docs_compile +} + +src_install() { + meson_src_install + + if use boinc; then + doappinfo "${FILESDIR}"/app_info_${PV}.xml + dowrapper ${PN}-boinc-zcp + + # install a blank file + insinto $(get_project_root) + insopts --owner boinc --group boinc + : newins - docking_out.sd + fi +} + +pkg_postinst() { + use boinc && boinc-app_pkg_postinst +} + +pkg_postrm() { + use boinc && boinc-app_pkg_postrm +} diff --git a/sci-biology/cmdock/files/app_info_0.1.4.xml b/sci-biology/cmdock/files/app_info_0.1.4.xml new file mode 100644 index 000000000..85dcdb16a --- /dev/null +++ b/sci-biology/cmdock/files/app_info_0.1.4.xml @@ -0,0 +1,37 @@ +<app_info> +<app> + <name>cmdock-boinc-zcp</name> + <user_friendly_name>CurieMarieDock on BOINC + zipped input, checkpoints and progress bar</user_friendly_name> +</app> + +<file_info> + <name>cmdock-boinc-zcp_wrapper_0.1.4</name> + <executable/> +</file_info> + +<file_info> + <name>cmdock-boinc-zcp_job_0.1.4.xml</name> +</file_info> +<file_info> + <name>docking_out.sd</name> +</file_info> + +<app_version> + <app_name>cmdock-boinc-zcp</app_name> + <version_num>200</version_num> + <file_ref> + <file_name>cmdock-boinc-zcp_wrapper_0.1.4</file_name> + <main_program/> + </file_ref> + <file_ref> + <file_name>cmdock-boinc-zcp_job_0.1.4.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-zcp_job_0.1.4.xml b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml new file mode 100644 index 000000000..074bb29d4 --- /dev/null +++ b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml @@ -0,0 +1,15 @@ +<job_desc> + <task> + <application>@PREFIX@/build/cmdock</application> + <stdout_filename>docking_log</stdout_filename> + <command_line>-c -j 1 -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@/build:$LD_LIBRARY_PATH</setenv> + <setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv> + </task> + <unzip_input> + <zipfilename>ligands.zip</zipfilename> + </unzip_input> +</job_desc> |