diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/cmdock/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/cmdock/cmdock-0.1.2.ebuild | 74 | ||||
| -rw-r--r-- | sci-biology/cmdock/cmdock-0.1.3.ebuild | 13 | ||||
| -rw-r--r-- | sci-biology/cmdock/files/app_info_0.1.2.xml | 66 | ||||
| -rw-r--r-- | sci-biology/cmdock/files/app_info_0.1.3.xml | 58 | ||||
| -rw-r--r-- | sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 14 | ||||
| -rw-r--r-- | sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml | 10 | ||||
| -rw-r--r-- | sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml | 10 |
8 files changed, 4 insertions, 242 deletions
diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest index c20f5e305..84968a8f8 100644 --- a/sci-biology/cmdock/Manifest +++ b/sci-biology/cmdock/Manifest @@ -1,2 +1 @@ -DIST cmdock-v0.1.2.tar.gz 13394195 BLAKE2B bd377b6a953d1e38b527da4eda36aee7a634e9f0c400487d4092ae1939589890038fc90052d8bddb25457dd027fa929acd50e836d65bd5994af89116f4c770a7 SHA512 90d4114a10dde99d34cd7ea4b28399da744cc295adebb10f1f9771b59841cd13e07cae5218643c90dd2847cdb014867ab795649a3d1883396a3609c3344b8226 DIST cmdock-v0.1.3.tar.gz 13416412 BLAKE2B abd6382943fb2ca2459fa493f8025e335821b96a95b88267dd493c28cd3280481b41ec6480fd3514cff126ab1077e89f075e5311393b1cd366403419e9c47454 SHA512 d941b672d14bad4fda4eaeb7aa313da1ade213241a1aee392747943a03afb6c66b3e93b8fd7eb9b1d8095b0632bd48cb062879cf445e3b54ce07069ad3087b22 diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild b/sci-biology/cmdock/cmdock-0.1.2.ebuild deleted file mode 100644 index 00934f81c..000000000 --- a/sci-biology/cmdock/cmdock-0.1.2.ebuild +++ /dev/null @@ -1,74 +0,0 @@ -# Copyright 2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..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" -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/pcg-cpp - dev-libs/cxxopts -" - -src_prepare() { - default - sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep = declare_dependency(include_directories: '/usr/include')|" -i meson.build || die -} - -src_configure() { - # very weird directory layout - local emesonargs=( - --prefix="${EPREFIX}/opt/cmdock-${PV}" - ) - meson_src_configure -} - -src_compile() { - meson_src_compile - docs_compile -} - -src_install() { - meson_src_install - - if use boinc ; then - insinto /var/lib/boinc/projects/www.sidock.si_sidock - newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml - doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml" - doins "${FILESDIR}/cmdock-boinc-zip_job_${PV}.xml" - - dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV} - dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV} - fi -} - -pkg_postinst() { - if use boinc ; then - touch /var/lib/boinc/projects/www.sidock.si_sidock/docking_out.sd || die - 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-0.1.3.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild index c4a2da7b4..e42b1f253 100644 --- a/sci-biology/cmdock/cmdock-0.1.3.ebuild +++ b/sci-biology/cmdock/cmdock-0.1.3.ebuild @@ -1,9 +1,9 @@ # Copyright 2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..10} pypy3 ) +PYTHON_COMPAT=( python3_{8..10} pypy3 ) DOCS_BUILDER="sphinx" DOCS_AUTODOC=0 DOCS_DIR="docs" @@ -26,14 +26,13 @@ RDEPEND=" BDEPEND=" dev-cpp/eigen:3 dev-cpp/indicators - dev-cpp/pcg-cpp + >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1 dev-libs/cxxopts " src_prepare() { default rm -r include/indicators || die - sed "s|pcg_cpp_dep = dependency.*|pcg_cpp_dep = declare_dependency(include_directories: '/usr/include')|" -i meson.build || die } src_configure() { @@ -55,13 +54,9 @@ src_install() { if use boinc ; then insinto /var/lib/boinc/projects/www.sidock.si_sidock newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml - doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml" doins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml" - newins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml" cmdock-boinc-zip_job_${PV}.xml - dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV} - dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV} - dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV} + dosym -r /usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV} fi } diff --git a/sci-biology/cmdock/files/app_info_0.1.2.xml b/sci-biology/cmdock/files/app_info_0.1.2.xml deleted file mode 100644 index f7575656b..000000000 --- a/sci-biology/cmdock/files/app_info_0.1.2.xml +++ /dev/null @@ -1,66 +0,0 @@ -<app_info> -<app> - <name>cmdock-boinc</name> - <user_friendly_name>CurieMarieDock on BOINC</user_friendly_name> -</app> -<app> - <name>cmdock-boinc-zip</name> - <user_friendly_name>CurieMarieDock on BOINC + zipped input</user_friendly_name> -</app> - -<file_info> - <name>cmdock-wrapper_0.1.2</name> - <executable/> -</file_info> -<file_info> - <name>cmdock-boinc-zip_wrapper_0.1.2</name> - <executable/> -</file_info> - -<file_info> - <name>cmdock-boinc_job_0.1.2.xml</name> -</file_info> -<file_info> - <name>cmdock-boinc-zip_job_0.1.2.xml</name> -</file_info> -<file_info> - <name>docking_out.sd</name> -</file_info> - -<app_version> - <app_name>cmdock-boinc</app_name> - <version_num>102</version_num> - <file_ref> - <file_name>cmdock-wrapper_0.1.2</file_name> - <main_program/> - </file_ref> - <file_ref> - <file_name>cmdock-boinc_job_0.1.2.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_version> - <app_name>cmdock-boinc-zip</app_name> - <version_num>204</version_num> - <file_ref> - <file_name>cmdock-boinc-zip_wrapper_0.1.2</file_name> - <main_program/> - </file_ref> - <file_ref> - <file_name>cmdock-boinc-zip_job_0.1.2.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/app_info_0.1.3.xml b/sci-biology/cmdock/files/app_info_0.1.3.xml index 5c901eba8..162ad0c05 100644 --- a/sci-biology/cmdock/files/app_info_0.1.3.xml +++ b/sci-biology/cmdock/files/app_info_0.1.3.xml @@ -1,62 +1,22 @@ <app_info> <app> - <name>cmdock-boinc</name> - <user_friendly_name>CurieMarieDock on BOINC</user_friendly_name> -</app> -<app> - <name>cmdock-boinc-zip</name> - <user_friendly_name>CurieMarieDock on BOINC + zipped input</user_friendly_name> -</app> -<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-wrapper_0.1.3</name> - <executable/> -</file_info> -<file_info> <name>cmdock-boinc-zcp_wrapper_0.1.3</name> <executable/> </file_info> -<file_info> - <name>cmdock-boinc-zip_wrapper_0.1.3</name> - <executable/> -</file_info> <file_info> - <name>cmdock-boinc_job_0.1.3.xml</name> -</file_info> -<file_info> <name>cmdock-boinc-zcp_job_0.1.3.xml</name> </file_info> <file_info> - <name>cmdock-boinc-zip_job_0.1.3.xml</name> -</file_info> -<file_info> <name>docking_out.sd</name> </file_info> <app_version> - <app_name>cmdock-boinc</app_name> - <version_num>103</version_num> - <file_ref> - <file_name>cmdock-wrapper_0.1.3</file_name> - <main_program/> - </file_ref> - <file_ref> - <file_name>cmdock-boinc_job_0.1.3.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_version> <app_name>cmdock-boinc-zcp</app_name> <version_num>100</version_num> <file_ref> @@ -74,22 +34,4 @@ <copy_file/> </file_ref> </app_version> -<app_version> - <app_name>cmdock-boinc-zip</app_name> - <version_num>300</version_num> - <file_ref> - <file_name>cmdock-boinc-zip_wrapper_0.1.3</file_name> - <main_program/> - </file_ref> - <file_ref> - <file_name>cmdock-boinc-zip_job_0.1.3.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-zip_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml deleted file mode 100644 index a11f1fe9b..000000000 --- a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml +++ /dev/null @@ -1,14 +0,0 @@ -<job_desc> - <task> - <application>/opt/cmdock-0.1.2/build/cmdock</application> - <stdout_filename>docking_log</stdout_filename> - <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> - <checkpoint_filename>docking_out.chk</checkpoint_filename> - <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv> - <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH</setenv> - <setenv>PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB</setenv> - </task> - <unzip_input> - <zipfilename>ligands.zip</zipfilename> - </unzip_input> -</job_desc> diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml deleted file mode 100644 index c670b677e..000000000 --- a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.2.xml +++ /dev/null @@ -1,10 +0,0 @@ -<job_desc> - <task> - <application>/opt/cmdock-0.1.2/build/cmdock</application> - <stdout_filename>docking_log</stdout_filename> - <command_line>-r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line> - <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv> - <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH</setenv> - <setenv>PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB</setenv> - </task> -</job_desc> diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml deleted file mode 100644 index 6082dc8fe..000000000 --- a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml +++ /dev/null @@ -1,10 +0,0 @@ -<job_desc> - <task> - <application>/opt/cmdock-0.1.3/build/cmdock</application> - <stdout_filename>docking_log</stdout_filename> - <command_line>-r target.prm -p /opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line> - <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.3</setenv> - <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv> - <setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv> - </task> -</job_desc> |