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sci-biology/cmdock: drop 0.1.3-r1
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
This commit is contained in:
Anna (cybertailor) Vyalkova
@@ -1,2 +1 @@
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DIST cmdock-v0.1.3.tar.gz 13416412 BLAKE2B abd6382943fb2ca2459fa493f8025e335821b96a95b88267dd493c28cd3280481b41ec6480fd3514cff126ab1077e89f075e5311393b1cd366403419e9c47454 SHA512 d941b672d14bad4fda4eaeb7aa313da1ade213241a1aee392747943a03afb6c66b3e93b8fd7eb9b1d8095b0632bd48cb062879cf445e3b54ce07069ad3087b22
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DIST cmdock-v0.1.4.tar.gz 14487352 BLAKE2B 3f212d596a12046f9a3b04376ca3e6d67f4391edba6f9c6e1fd372e7c7dbb23727ebd77787f125e57afca16e0cffc9b734dcdc7a83a825c52737218df371cbfd SHA512 6e1a366d82b311da0fdcd99ecf3e10962073453c7fdec9142854d472336f7f918bb76368b52e5904bf30e0aea6b8476a3ab522469daeaef52293ac481741b4bb
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@@ -1,98 +0,0 @@
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# Copyright 2021 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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PYTHON_COMPAT=( python3_{8..10} pypy3 )
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BOINC_APP_OPTIONAL="true"
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DOCS_BUILDER="sphinx"
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DOCS_AUTODOC=0
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DOCS_DIR="docs"
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inherit python-any-r1 boinc-app docs meson
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DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
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HOMEPAGE="https://gitlab.com/Jukic/cmdock https://www.rxdock.org"
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SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz"
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S="${WORKDIR}/${PN}-v${PV}"
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LICENSE="LGPL-3"
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SLOT="0/${PV}"
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KEYWORDS="~amd64"
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IUSE="apidoc boinc"
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REQUIRED_USE="apidoc? ( doc )"
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RDEPEND="
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dev-lang/perl
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boinc? ( sci-misc/boinc-wrapper )
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"
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BDEPEND="
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dev-cpp/eigen:3
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dev-cpp/indicators
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>=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
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dev-libs/cxxopts
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apidoc? ( app-doc/doxygen )
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"
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DOCS=( INSTALL.md README.md )
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BOINC_MASTER_URL="https://www.sidock.si/sidock/"
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BOINC_INVITATION_CODE="Crunch_4Science"
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BOINC_APP_HELPTEXT=\
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"The easiest way to do something useful with this application
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is to attach it to SiDock@home BOINC project."
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foreach_wrapper_job() {
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sed -i "$1" \
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-e "s:@PREFIX@:${EPREFIX}/opt/${P}:g" || die
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}
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src_prepare() {
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default
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rm -r include/indicators || die
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}
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src_configure() {
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# very weird directory layout
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local emesonargs=(
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--prefix="${EPREFIX}/opt/${P}"
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)
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meson_src_configure
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}
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src_compile() {
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meson_src_compile
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# subshell prevents from overriding global
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# DOCS_BUILDER and DOCS_OUTDIR
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use apidoc && (
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DOCS_BUILDER="doxygen"
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DOCS_OUTDIR="${S}/_build/html/api"
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docs_compile
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)
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docs_compile
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}
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src_install() {
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meson_src_install
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if use boinc; then
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doappinfo "${FILESDIR}"/app_info_${PV}.xml
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dowrapper ${PN}-boinc-zcp
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# install a blank file
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insinto $(get_project_root)
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insopts --owner boinc --group boinc
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: newins - docking_out.sd
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fi
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}
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pkg_postinst() {
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use boinc && boinc-app_pkg_postinst
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}
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pkg_postrm() {
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use boinc && boinc-app_pkg_postrm
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}
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@@ -1,37 +0,0 @@
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<app_info>
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<app>
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<name>cmdock-boinc-zcp</name>
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<user_friendly_name>CurieMarieDock on BOINC + zipped input, checkpoints and progress bar</user_friendly_name>
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</app>
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<file_info>
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<name>cmdock-boinc-zcp_wrapper_0.1.3</name>
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<executable/>
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</file_info>
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<file_info>
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<name>cmdock-boinc-zcp_job_0.1.3.xml</name>
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</file_info>
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<file_info>
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<name>docking_out.sd</name>
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</file_info>
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<app_version>
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<app_name>cmdock-boinc-zcp</app_name>
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<version_num>100</version_num>
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<file_ref>
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<file_name>cmdock-boinc-zcp_wrapper_0.1.3</file_name>
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<main_program/>
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</file_ref>
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<file_ref>
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<file_name>cmdock-boinc-zcp_job_0.1.3.xml</file_name>
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<open_name>job.xml</open_name>
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<copy_file/>
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</file_ref>
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<file_ref>
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<file_name>docking_out.sd</file_name>
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<open_name>docking_out.sd</open_name>
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<copy_file/>
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</file_ref>
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</app_version>
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</app_info>
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@@ -1,15 +0,0 @@
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<job_desc>
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<task>
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<application>@PREFIX@/build/cmdock</application>
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<stdout_filename>docking_log</stdout_filename>
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<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>
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<checkpoint_filename>docking_out.chk</checkpoint_filename>
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<fraction_done_filename>docking_out.progress</fraction_done_filename>
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<setenv>CMDOCK_ROOT=@PREFIX@</setenv>
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<setenv>LD_LIBRARY_PATH=@PREFIX@/build:$LD_LIBRARY_PATH</setenv>
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<setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv>
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</task>
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<unzip_input>
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<zipfilename>ligands.zip</zipfilename>
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</unzip_input>
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</job_desc>
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