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sci-biology/cmdock: fixes
Bug: https://bugs.gentoo.org/979500 Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo@sysrq.in>
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Anna (cybertailor) Vyalkova committed
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@@ -1,118 +0,0 @@
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# Copyright 2021-2024 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_12 )
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BOINC_APP_OPTIONAL=1
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inherit boinc-app flag-o-matic meson optfeature python-any-r1
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DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
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HOMEPAGE="https://gitlab.com/Jukic/cmdock"
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SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.bz2"
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S="${WORKDIR}/${PN}-v${PV}"
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LICENSE="LGPL-3 ZLIB"
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SLOT="0/${PV}"
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KEYWORDS="~amd64"
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IUSE="apidoc cpu_flags_x86_sse2 doc test"
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# Flaky tests
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RESTRICT="test"
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DEPEND="
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dev-cpp/eigen:3
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>=dev-cpp/indicators-2.3-r1
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>=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
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>=dev-libs/cxxopts-3
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"
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BDEPEND="
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apidoc? (
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app-text/doxygen
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dev-texlive/texlive-fontutils
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)
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doc? (
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$(python_gen_any_dep '
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dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]
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dev-python/sphinx[${PYTHON_USEDEP}]
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')
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)
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test? ( ${PYTHON_DEPS} )
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"
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PATCHES=(
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"${FILESDIR}"/${P}-include.patch
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"${FILESDIR}"/${P}-cxxopts.patch
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)
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DOCS=( README.md changelog.md )
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BOINC_MASTER_URL="https://www.sidock.si/sidock/"
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BOINC_INVITATION_CODE="Crunch_4Science"
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BOINC_APP_HELPTEXT=\
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"The easiest way to do something useful with this application
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is to attach it to SiDock@home BOINC project."
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INSTALL_PREFIX="${EPREFIX}/opt/${P}"
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boinc-app_add_deps
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python_check_deps() {
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use doc || return 0
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python_has_version "dev-python/sphinx[${PYTHON_USEDEP}]" &&
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python_has_version "dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]"
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}
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foreach_wrapper_job() {
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sed -e "s:@PREFIX@:${INSTALL_PREFIX}:g" -i "${1}" || die
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}
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src_prepare() {
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default
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python_fix_shebang "${S}"/bin
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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="${INSTALL_PREFIX:?}"
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$(meson_use apidoc)
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$(meson_use doc)
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$(meson_use test tests)
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-Ddocdir="${EPREFIX}"/usr/share/doc/${PF}
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)
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meson_src_configure
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use cpu_flags_x86_sse2 || append-cppflags "-DBUNDLE_NO_SSE"
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}
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src_install() {
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meson_src_install
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python_optimize "${D}${INSTALL_PREFIX:?}"/bin
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if use boinc; then
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boinc_install_appinfo "${FILESDIR}"/app_info_0.2.0-r1.xml
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boinc_install_wrapper cmdock-l_wrapper \
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"${FILESDIR}"/cmdock-l_job_0.2.0-r1.xml cmdock-l_job.xml
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# install cmdock executable
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exeinto "$(get_project_root)"
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exeopts --owner root --group boinc
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doexe "${D}${INSTALL_PREFIX:?}"/bin/cmdock
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# install a blank file
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insinto "$(get_project_root)"
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insopts -m 0644 --owner root --group boinc
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newins - docking_out
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fi
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}
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pkg_postinst() {
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optfeature "sdtether.py and sdrmsd.py scripts" "dev-python/numpy sci-chemistry/openbabel[python]"
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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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+26
-10
@@ -3,7 +3,7 @@
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EAPI=8
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PYTHON_COMPAT=( python3_{12..13} )
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PYTHON_COMPAT=( python3_{12..14} )
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BOINC_APP_OPTIONAL=1
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inherit boinc-app flag-o-matic meson optfeature python-any-r1
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@@ -13,18 +13,20 @@ SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.bz2"
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S="${WORKDIR}/${PN}-v${PV}"
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LICENSE="LGPL-3 ZLIB"
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SLOT="0/${PV}"
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SLOT="0"
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KEYWORDS="~amd64"
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IUSE="apidoc cpu_flags_x86_sse2 doc test"
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# Flaky tests
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RESTRICT="test"
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RDEPEND="dev-libs/icu:="
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DEPEND="
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${RDEPEND}
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dev-cpp/eigen:3
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>=dev-cpp/indicators-2.3-r1
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>=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
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>=dev-libs/cxxopts-3
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>=dev-libs/cxxopts-3.1[icu]
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"
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BDEPEND="
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apidoc? (
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@@ -48,7 +50,6 @@ PATCHES=(
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DOCS=( README.md changelog.md )
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BOINC_MASTER_URL="https://www.sidock.si/sidock/"
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BOINC_INVITATION_CODE="Crunch_4Science"
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BOINC_APP_HELPTEXT=\
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"The easiest way to do something useful with this application
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is to attach it to SiDock@home BOINC project."
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@@ -74,13 +75,28 @@ src_prepare() {
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}
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src_configure() {
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# very weird directory layout
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mkdir "${T}/pkg-config" || die
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export PKG_CONFIG_PATH="${T}/pkg-config${PKG_CONFIG_PATH+:${PKG_CONFIG_PATH}}"
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cat >> "${T}/pkg-config/pcg-cpp.pc" <<-EOF || die
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Name: pcg-cpp
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Version: 9999
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Description:
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EOF
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cat >> "${T}/pkg-config/icu-cu.pc" <<-EOF || die
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Name: icu-cu
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Version: 9999
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Description:
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Requires: icu-uc
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EOF
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# extremely weird directory layout
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local emesonargs=(
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--prefix="${INSTALL_PREFIX:?}"
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$(meson_use apidoc)
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$(meson_use doc)
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$(meson_use test tests)
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-Ddocdir="${EPREFIX}"/usr/share/doc/${PF}
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-Dcpp_std=c++17
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)
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meson_src_configure
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@@ -92,16 +108,16 @@ src_install() {
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python_optimize "${D}${INSTALL_PREFIX:?}"/bin
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if use boinc; then
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boinc_install_appinfo "${FILESDIR}"/app_info_0.2.0-r1.xml
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boinc_install_wrapper cmdock-l_wrapper \
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"${FILESDIR}"/cmdock-l_job_0.2.0-r1.xml cmdock-l_job.xml
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boinc_install_appinfo "${FILESDIR}"/app_info_0.2.0-r2.xml
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boinc_install_wrapper cmdock_wrapper \
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"${FILESDIR}"/sidock_job_0.2.0.xml sidock_job.xml
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# install cmdock executable
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# install the main executable
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exeinto "$(get_project_root)"
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exeopts --owner root --group boinc
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doexe "${D}${INSTALL_PREFIX:?}"/bin/cmdock
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# install a blank file
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# install an empty file
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insinto "$(get_project_root)"
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insopts -m 0644 --owner root --group boinc
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newins - docking_out
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+9
-8
@@ -1,11 +1,11 @@
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<app_info>
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<app>
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<name>cmdock-l</name>
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<user_friendly_name>CurieMarieDock @PV@ long tasks</user_friendly_name>
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<name>sidock</name>
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<user_friendly_name>SiDock@home CurieMarieDock</user_friendly_name>
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</app>
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<file_info>
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<name>cmdock-l_wrapper</name>
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<name>cmdock_wrapper</name>
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<sticky/>
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<executable/>
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</file_info>
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@@ -16,7 +16,7 @@
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</file_info>
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<file_info>
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<name>cmdock-l_job.xml</name>
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<name>sidock_job.xml</name>
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<sticky/>
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</file_info>
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<file_info>
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@@ -25,19 +25,19 @@
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</file_info>
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<app_version>
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<app_name>cmdock-l</app_name>
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<app_name>sidock</app_name>
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<version_num>100</version_num>
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<file_ref>
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<file_name>cmdock-l_wrapper</file_name>
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<file_name>cmdock_wrapper</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</file_name>
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<open_name>cmdock</open_name>
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<open_name>sidock</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>cmdock-l_job.xml</file_name>
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<file_name>sidock_job.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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@@ -46,5 +46,6 @@
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<open_name>docking_out</open_name>
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<copy_file/>
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</file_ref>
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<is_wrapper/>
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</app_version>
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</app_info>
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+1
-1
@@ -1,6 +1,6 @@
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<job_desc>
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<task>
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<application>cmdock</application>
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<application>sidock</application>
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<stdout_filename>docking_log</stdout_filename>
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<command_line>-c -j 1 -b 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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@@ -7,7 +7,7 @@
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</maintainer>
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<upstream>
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<remote-id type="gitlab">Jukic/cmdock</remote-id>
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<bugs-to>https://gitlab.com/Jukic/cmdock/-/issues</bugs-to>
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<bugs-to>https://gitlab.com/Jukic/cmdock/-/work_items</bugs-to>
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<doc>https://rxdock.gitlab.io/documentation/devel/html/</doc>
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</upstream>
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<use>
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