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commit: eb972dae4900efd571efe420cf683200a997d924 |
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Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in> |
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AuthorDate: Sun Jun 27 08:51:43 2021 +0000 |
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Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in> |
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CommitDate: Thu Jul 1 04:58:25 2021 +0000 |
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URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=eb972dae |
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|
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sci-biology/cmdock: drop obsolete |
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|
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Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in> |
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|
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sci-biology/cmdock/Manifest | 1 - |
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sci-biology/cmdock/cmdock-0.1.2.ebuild | 74 ---------------------- |
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sci-biology/cmdock/cmdock-0.1.3.ebuild | 13 ++-- |
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sci-biology/cmdock/files/app_info_0.1.2.xml | 66 ------------------- |
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sci-biology/cmdock/files/app_info_0.1.3.xml | 58 ----------------- |
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.../cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 14 ---- |
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.../cmdock/files/cmdock-boinc_job_0.1.2.xml | 10 --- |
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.../cmdock/files/cmdock-boinc_job_0.1.3.xml | 10 --- |
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8 files changed, 4 insertions(+), 242 deletions(-) |
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|
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diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest |
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index c20f5e305..84968a8f8 100644 |
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--- a/sci-biology/cmdock/Manifest |
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+++ b/sci-biology/cmdock/Manifest |
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@@ -1,2 +1 @@ |
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-DIST cmdock-v0.1.2.tar.gz 13394195 BLAKE2B bd377b6a953d1e38b527da4eda36aee7a634e9f0c400487d4092ae1939589890038fc90052d8bddb25457dd027fa929acd50e836d65bd5994af89116f4c770a7 SHA512 90d4114a10dde99d34cd7ea4b28399da744cc295adebb10f1f9771b59841cd13e07cae5218643c90dd2847cdb014867ab795649a3d1883396a3609c3344b8226 |
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DIST cmdock-v0.1.3.tar.gz 13416412 BLAKE2B abd6382943fb2ca2459fa493f8025e335821b96a95b88267dd493c28cd3280481b41ec6480fd3514cff126ab1077e89f075e5311393b1cd366403419e9c47454 SHA512 d941b672d14bad4fda4eaeb7aa313da1ade213241a1aee392747943a03afb6c66b3e93b8fd7eb9b1d8095b0632bd48cb062879cf445e3b54ce07069ad3087b22 |
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|
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diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild b/sci-biology/cmdock/cmdock-0.1.2.ebuild |
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deleted file mode 100644 |
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index 00934f81c..000000000 |
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--- a/sci-biology/cmdock/cmdock-0.1.2.ebuild |
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+++ /dev/null |
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@@ -1,74 +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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- |
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-EAPI=7 |
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- |
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-PYTHON_COMPAT=( python3_{7..10} pypy3 ) |
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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 docs meson |
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- |
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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.gz" |
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-S="${WORKDIR}/${PN}-v${PV}" |
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- |
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-LICENSE="LGPL-3" |
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-SLOT="0/${PV}" |
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-KEYWORDS="~amd64" |
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-IUSE="boinc" |
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- |
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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/pcg-cpp |
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- dev-libs/cxxopts |
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-" |
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- |
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-src_prepare() { |
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- default |
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- sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep = declare_dependency(include_directories: '/usr/include')|" -i meson.build || die |
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-} |
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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="${EPREFIX}/opt/cmdock-${PV}" |
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- ) |
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- meson_src_configure |
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-} |
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- |
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-src_compile() { |
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- meson_src_compile |
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- docs_compile |
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-} |
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- |
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-src_install() { |
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- meson_src_install |
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- |
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- if use boinc ; then |
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- insinto /var/lib/boinc/projects/www.sidock.si_sidock |
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- newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml |
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- doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml" |
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- doins "${FILESDIR}/cmdock-boinc-zip_job_${PV}.xml" |
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- |
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- dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV} |
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- dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV} |
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- fi |
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-} |
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- |
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-pkg_postinst() { |
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- if use boinc ; then |
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- touch /var/lib/boinc/projects/www.sidock.si_sidock/docking_out.sd || die |
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- elog |
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- elog "The easiest way to do something useful with this application" |
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- elog "is to attach it to SiDock@home BOINC project." |
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- elog |
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- elog "- Master URL: https://sidock.si/sidock/" |
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- elog "- Invitation code: Crunch_4Science" |
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- fi |
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-} |
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|
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diff --git a/sci-biology/cmdock/cmdock-0.1.3.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild |
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index c4a2da7b4..e42b1f253 100644 |
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--- a/sci-biology/cmdock/cmdock-0.1.3.ebuild |
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+++ b/sci-biology/cmdock/cmdock-0.1.3.ebuild |
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@@ -1,9 +1,9 @@ |
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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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|
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-EAPI=7 |
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+EAPI=8 |
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|
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-PYTHON_COMPAT=( python3_{7..10} pypy3 ) |
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+PYTHON_COMPAT=( python3_{8..10} pypy3 ) |
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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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@@ -26,14 +26,13 @@ RDEPEND=" |
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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 |
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+ >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1 |
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dev-libs/cxxopts |
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" |
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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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- sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep = declare_dependency(include_directories: '/usr/include')|" -i meson.build || die |
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} |
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|
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src_configure() { |
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@@ -55,13 +54,9 @@ src_install() { |
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if use boinc ; then |
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insinto /var/lib/boinc/projects/www.sidock.si_sidock |
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newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml |
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- doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml" |
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doins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml" |
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- newins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml" cmdock-boinc-zip_job_${PV}.xml |
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|
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- dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV} |
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- dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV} |
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- dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV} |
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+ dosym -r /usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV} |
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fi |
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} |
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|
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|
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diff --git a/sci-biology/cmdock/files/app_info_0.1.2.xml b/sci-biology/cmdock/files/app_info_0.1.2.xml |
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deleted file mode 100644 |
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index f7575656b..000000000 |
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--- a/sci-biology/cmdock/files/app_info_0.1.2.xml |
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+++ /dev/null |
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@@ -1,66 +0,0 @@ |
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-<app_info> |
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-<app> |
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- <name>cmdock-boinc</name> |
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- <user_friendly_name>CurieMarieDock on BOINC</user_friendly_name> |
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-</app> |
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-<app> |
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- <name>cmdock-boinc-zip</name> |
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- <user_friendly_name>CurieMarieDock on BOINC + zipped input</user_friendly_name> |
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-</app> |
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- |
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-<file_info> |
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- <name>cmdock-wrapper_0.1.2</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-zip_wrapper_0.1.2</name> |
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- <executable/> |
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-</file_info> |
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- |
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-<file_info> |
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- <name>cmdock-boinc_job_0.1.2.xml</name> |
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-</file_info> |
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-<file_info> |
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- <name>cmdock-boinc-zip_job_0.1.2.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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- |
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-<app_version> |
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- <app_name>cmdock-boinc</app_name> |
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- <version_num>102</version_num> |
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- <file_ref> |
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- <file_name>cmdock-wrapper_0.1.2</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_job_0.1.2.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_version> |
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- <app_name>cmdock-boinc-zip</app_name> |
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- <version_num>204</version_num> |
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- <file_ref> |
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- <file_name>cmdock-boinc-zip_wrapper_0.1.2</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-zip_job_0.1.2.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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|
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diff --git a/sci-biology/cmdock/files/app_info_0.1.3.xml b/sci-biology/cmdock/files/app_info_0.1.3.xml |
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index 5c901eba8..162ad0c05 100644 |
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--- a/sci-biology/cmdock/files/app_info_0.1.3.xml |
235 |
+++ b/sci-biology/cmdock/files/app_info_0.1.3.xml |
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@@ -1,61 +1,21 @@ |
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<app_info> |
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-<app> |
239 |
- <name>cmdock-boinc</name> |
240 |
- <user_friendly_name>CurieMarieDock on BOINC</user_friendly_name> |
241 |
-</app> |
242 |
-<app> |
243 |
- <name>cmdock-boinc-zip</name> |
244 |
- <user_friendly_name>CurieMarieDock on BOINC + zipped input</user_friendly_name> |
245 |
-</app> |
246 |
<app> |
247 |
<name>cmdock-boinc-zcp</name> |
248 |
<user_friendly_name>CurieMarieDock on BOINC + zipped input, checkpoints and progress bar</user_friendly_name> |
249 |
</app> |
250 |
|
251 |
-<file_info> |
252 |
- <name>cmdock-wrapper_0.1.3</name> |
253 |
- <executable/> |
254 |
-</file_info> |
255 |
<file_info> |
256 |
<name>cmdock-boinc-zcp_wrapper_0.1.3</name> |
257 |
<executable/> |
258 |
</file_info> |
259 |
-<file_info> |
260 |
- <name>cmdock-boinc-zip_wrapper_0.1.3</name> |
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- <executable/> |
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-</file_info> |
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|
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-<file_info> |
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- <name>cmdock-boinc_job_0.1.3.xml</name> |
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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> |
269 |
</file_info> |
270 |
-<file_info> |
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- <name>cmdock-boinc-zip_job_0.1.3.xml</name> |
272 |
-</file_info> |
273 |
<file_info> |
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<name>docking_out.sd</name> |
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</file_info> |
276 |
|
277 |
-<app_version> |
278 |
- <app_name>cmdock-boinc</app_name> |
279 |
- <version_num>103</version_num> |
280 |
- <file_ref> |
281 |
- <file_name>cmdock-wrapper_0.1.3</file_name> |
282 |
- <main_program/> |
283 |
- </file_ref> |
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- <file_ref> |
285 |
- <file_name>cmdock-boinc_job_0.1.3.xml</file_name> |
286 |
- <open_name>job.xml</open_name> |
287 |
- <copy_file/> |
288 |
- </file_ref> |
289 |
- <file_ref> |
290 |
- <file_name>docking_out.sd</file_name> |
291 |
- <open_name>docking_out.sd</open_name> |
292 |
- <copy_file/> |
293 |
- </file_ref> |
294 |
-</app_version> |
295 |
<app_version> |
296 |
<app_name>cmdock-boinc-zcp</app_name> |
297 |
<version_num>100</version_num> |
298 |
@@ -74,22 +34,4 @@ |
299 |
<copy_file/> |
300 |
</file_ref> |
301 |
</app_version> |
302 |
-<app_version> |
303 |
- <app_name>cmdock-boinc-zip</app_name> |
304 |
- <version_num>300</version_num> |
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- <file_ref> |
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- <file_name>cmdock-boinc-zip_wrapper_0.1.3</file_name> |
307 |
- <main_program/> |
308 |
- </file_ref> |
309 |
- <file_ref> |
310 |
- <file_name>cmdock-boinc-zip_job_0.1.3.xml</file_name> |
311 |
- <open_name>job.xml</open_name> |
312 |
- <copy_file/> |
313 |
- </file_ref> |
314 |
- <file_ref> |
315 |
- <file_name>docking_out.sd</file_name> |
316 |
- <open_name>docking_out.sd</open_name> |
317 |
- <copy_file/> |
318 |
- </file_ref> |
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-</app_version> |
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</app_info> |
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|
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diff --git a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml |
323 |
deleted file mode 100644 |
324 |
index a11f1fe9b..000000000 |
325 |
--- a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml |
326 |
+++ /dev/null |
327 |
@@ -1,14 +0,0 @@ |
328 |
-<job_desc> |
329 |
- <task> |
330 |
- <application>/opt/cmdock-0.1.2/build/cmdock</application> |
331 |
- <stdout_filename>docking_log</stdout_filename> |
332 |
- <command_line>-c -r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line> |
333 |
- <checkpoint_filename>docking_out.chk</checkpoint_filename> |
334 |
- <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv> |
335 |
- <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH</setenv> |
336 |
- <setenv>PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB</setenv> |
337 |
- </task> |
338 |
- <unzip_input> |
339 |
- <zipfilename>ligands.zip</zipfilename> |
340 |
- </unzip_input> |
341 |
-</job_desc> |
342 |
|
343 |
diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml |
344 |
deleted file mode 100644 |
345 |
index c670b677e..000000000 |
346 |
--- a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml |
347 |
+++ /dev/null |
348 |
@@ -1,10 +0,0 @@ |
349 |
-<job_desc> |
350 |
- <task> |
351 |
- <application>/opt/cmdock-0.1.2/build/cmdock</application> |
352 |
- <stdout_filename>docking_log</stdout_filename> |
353 |
- <command_line>-r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line> |
354 |
- <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv> |
355 |
- <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH</setenv> |
356 |
- <setenv>PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB</setenv> |
357 |
- </task> |
358 |
-</job_desc> |
359 |
|
360 |
diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml |
361 |
deleted file mode 100644 |
362 |
index 6082dc8fe..000000000 |
363 |
--- a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml |
364 |
+++ /dev/null |
365 |
@@ -1,10 +0,0 @@ |
366 |
-<job_desc> |
367 |
- <task> |
368 |
- <application>/opt/cmdock-0.1.3/build/cmdock</application> |
369 |
- <stdout_filename>docking_log</stdout_filename> |
370 |
- <command_line>-r target.prm -p /opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line> |
371 |
- <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.3</setenv> |
372 |
- <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv> |
373 |
- <setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv> |
374 |
- </task> |
375 |
-</job_desc> |