commit: eb972dae4900efd571efe420cf683200a997d924
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Sun Jun 27 08:51:43 2021 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Thu Jul 1 04:58:25 2021 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=eb972dae
sci-biology/cmdock: drop obsolete
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/Manifest | 1 -
sci-biology/cmdock/cmdock-0.1.2.ebuild | 74 ----------------------
sci-biology/cmdock/cmdock-0.1.3.ebuild | 13 ++--
sci-biology/cmdock/files/app_info_0.1.2.xml | 66 -------------------
sci-biology/cmdock/files/app_info_0.1.3.xml | 58 -----------------
.../cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 14 ----
.../cmdock/files/cmdock-boinc_job_0.1.2.xml | 10 ---
.../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
@@ -1,61 +1,21 @@
<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>
@@ -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>
