* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/
@ 2021-05-20 12:47 Anna Vyalkova
0 siblings, 0 replies; 8+ messages in thread
From: Anna Vyalkova @ 2021-05-20 12:47 UTC (permalink / raw
To: gentoo-commits
commit: 1883f124c2d77a9648dae60406fb1e956186af04
Author: Anna Vyalkova <cyber <AT> sysrq <DOT> in>
AuthorDate: Thu May 20 12:26:42 2021 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Thu May 20 12:47:26 2021 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=1883f124
sci-biology/cmdock: fixes in deps and app_info.xml
1) Python is only used by Sphinx to build documentation
2) Rename app_config.xml to app_info.xml:
https://boinc.berkeley.edu/wiki/Anonymous_platform
Signed-off-by: Anna Vyalkova <cyber <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.1.2.ebuild | 7 ++++---
sci-biology/cmdock/files/{app_config.xml => app_info.xml} | 0
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild b/sci-biology/cmdock/cmdock-0.1.2.ebuild
index 03f3d769e..aa5a4546b 100644
--- a/sci-biology/cmdock/cmdock-0.1.2.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.2.ebuild
@@ -19,12 +19,13 @@ SLOT="${PV}"
KEYWORDS="~amd64"
IUSE="boinc"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+REQUIRED_USE="doc? ( ${PYTHON_REQUIRED_USE} )"
-DEPEND="${PYTHON_DEPS}
+DEPEND="
dev-cpp/eigen
dev-libs/cxxopts
boinc? ( sci-misc/boinc-wrapper )
+ doc? ( ${PYTHON_DEPS} )
"
RDEPEND="${DEPEND}
dev-lang/perl
@@ -54,7 +55,7 @@ src_install() {
if use boinc ; then
insinto /var/lib/boinc/projects/www.sidock.si_sidock
- doins "${FILESDIR}/app_config.xml"
+ doins "${FILESDIR}/app_info.xml"
doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml"
doins "${FILESDIR}/cmdock-boinc-zip_job_${PV}.xml"
diff --git a/sci-biology/cmdock/files/app_config.xml b/sci-biology/cmdock/files/app_info.xml
similarity index 100%
rename from sci-biology/cmdock/files/app_config.xml
rename to sci-biology/cmdock/files/app_info.xml
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/
@ 2021-05-29 15:49 Anna Vyalkova
0 siblings, 0 replies; 8+ messages in thread
From: Anna Vyalkova @ 2021-05-29 15:49 UTC (permalink / raw
To: gentoo-commits
commit: aba20d3142c80878bbc1a3b045f14c849a63cb63
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Sat May 29 13:37:10 2021 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Sat May 29 15:48:30 2021 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=aba20d31
sci-biology/cmdock: add 0.1.3
* revise deps
* fix symlinks
* replace slotting with subslotting
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/Manifest | 1 +
sci-biology/cmdock/cmdock-0.1.2.ebuild | 29 +++----
.../{cmdock-0.1.2.ebuild => cmdock-0.1.3.ebuild} | 35 ++++----
.../files/{app_info.xml => app_info_0.1.2.xml} | 2 +-
sci-biology/cmdock/files/app_info_0.1.3.xml | 95 ++++++++++++++++++++++
.../cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml | 15 ++++
.../cmdock/files/cmdock-boinc-zip_job_0.1.2.xml | 3 +-
.../cmdock/files/cmdock-boinc_job_0.1.3.xml | 10 +++
8 files changed, 155 insertions(+), 35 deletions(-)
diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
index 25663d438..c20f5e305 100644
--- a/sci-biology/cmdock/Manifest
+++ b/sci-biology/cmdock/Manifest
@@ -1 +1,2 @@
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
index aa5a4546b..00934f81c 100644
--- a/sci-biology/cmdock/cmdock-0.1.2.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.2.ebuild
@@ -3,34 +3,31 @@
EAPI=7
-PYTHON_COMPAT=( python3_{7..9} pypy3 )
+PYTHON_COMPAT=( python3_{7..10} pypy3 )
DOCS_BUILDER="sphinx"
DOCS_AUTODOC=0
-inherit python-r1 docs meson
+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${PV}"
-DOCS_DIR="${S}/docs"
LICENSE="LGPL-3"
-SLOT="${PV}"
+SLOT="0/${PV}"
KEYWORDS="~amd64"
-
IUSE="boinc"
-REQUIRED_USE="doc? ( ${PYTHON_REQUIRED_USE} )"
-DEPEND="
- dev-cpp/eigen
- dev-libs/cxxopts
+RDEPEND="
+ dev-lang/perl
boinc? ( sci-misc/boinc-wrapper )
- doc? ( ${PYTHON_DEPS} )
"
-RDEPEND="${DEPEND}
- dev-lang/perl
+BDEPEND="
+ dev-cpp/eigen:3
+ dev-cpp/pcg-cpp
+ dev-libs/cxxopts
"
-BDEPEND="dev-cpp/pcg-cpp"
src_prepare() {
default
@@ -55,12 +52,12 @@ src_install() {
if use boinc ; then
insinto /var/lib/boinc/projects/www.sidock.si_sidock
- doins "${FILESDIR}/app_info.xml"
+ newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml
doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml"
doins "${FILESDIR}/cmdock-boinc-zip_job_${PV}.xml"
- dosym "${EPREFIX}"/usr/bin/boinc-wrapper "/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}"
- dosym "${EPREFIX}"/usr/bin/boinc-wrapper "/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}"
+ dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}
+ dosym ../../../../../usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}
fi
}
diff --git a/sci-biology/cmdock/cmdock-0.1.2.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild
similarity index 64%
copy from sci-biology/cmdock/cmdock-0.1.2.ebuild
copy to sci-biology/cmdock/cmdock-0.1.3.ebuild
index aa5a4546b..c4a2da7b4 100644
--- a/sci-biology/cmdock/cmdock-0.1.2.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.3.ebuild
@@ -3,37 +3,36 @@
EAPI=7
-PYTHON_COMPAT=( python3_{7..9} pypy3 )
+PYTHON_COMPAT=( python3_{7..10} pypy3 )
DOCS_BUILDER="sphinx"
DOCS_AUTODOC=0
-inherit python-r1 docs meson
+DOCS_DIR="docs"
+inherit python-any-r1 docs meson
DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
HOMEPAGE="https://gitlab.com/Jukic/cmdock"
SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz"
S="${WORKDIR}/${PN}-v${PV}"
-DOCS_DIR="${S}/docs"
LICENSE="LGPL-3"
-SLOT="${PV}"
+SLOT="0/${PV}"
KEYWORDS="~amd64"
-
IUSE="boinc"
-REQUIRED_USE="doc? ( ${PYTHON_REQUIRED_USE} )"
-DEPEND="
- dev-cpp/eigen
- dev-libs/cxxopts
+RDEPEND="
+ dev-lang/perl
boinc? ( sci-misc/boinc-wrapper )
- doc? ( ${PYTHON_DEPS} )
"
-RDEPEND="${DEPEND}
- dev-lang/perl
+BDEPEND="
+ dev-cpp/eigen:3
+ dev-cpp/indicators
+ dev-cpp/pcg-cpp
+ dev-libs/cxxopts
"
-BDEPEND="dev-cpp/pcg-cpp"
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
}
@@ -55,12 +54,14 @@ src_install() {
if use boinc ; then
insinto /var/lib/boinc/projects/www.sidock.si_sidock
- doins "${FILESDIR}/app_info.xml"
+ newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml
doins "${FILESDIR}/cmdock-boinc_job_${PV}.xml"
- doins "${FILESDIR}/cmdock-boinc-zip_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 "${EPREFIX}"/usr/bin/boinc-wrapper "/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-wrapper_${PV}"
- dosym "${EPREFIX}"/usr/bin/boinc-wrapper "/var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zip_wrapper_${PV}"
+ 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}
fi
}
diff --git a/sci-biology/cmdock/files/app_info.xml b/sci-biology/cmdock/files/app_info_0.1.2.xml
similarity index 97%
rename from sci-biology/cmdock/files/app_info.xml
rename to sci-biology/cmdock/files/app_info_0.1.2.xml
index eb222052b..f7575656b 100644
--- a/sci-biology/cmdock/files/app_info.xml
+++ b/sci-biology/cmdock/files/app_info_0.1.2.xml
@@ -47,7 +47,7 @@
</app_version>
<app_version>
<app_name>cmdock-boinc-zip</app_name>
- <version_num>200</version_num>
+ <version_num>204</version_num>
<file_ref>
<file_name>cmdock-boinc-zip_wrapper_0.1.2</file_name>
<main_program/>
diff --git a/sci-biology/cmdock/files/app_info_0.1.3.xml b/sci-biology/cmdock/files/app_info_0.1.3.xml
new file mode 100644
index 000000000..5c901eba8
--- /dev/null
+++ b/sci-biology/cmdock/files/app_info_0.1.3.xml
@@ -0,0 +1,95 @@
+<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>
+ <file_name>cmdock-boinc-zcp_wrapper_0.1.3</file_name>
+ <main_program/>
+ </file_ref>
+ <file_ref>
+ <file_name>cmdock-boinc-zcp_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-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-zcp_job_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
new file mode 100644
index 000000000..3c7818151
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
@@ -0,0 +1,15 @@
+<job_desc>
+ <task>
+ <application>/opt/cmdock-0.1.3/build/cmdock</application>
+ <stdout_filename>docking_log</stdout_filename>
+ <command_line>-c -j 1 -r target.prm -p /opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+ <checkpoint_filename>docking_out.chk</checkpoint_filename>
+ <fraction_done_filename>docking_out.progress</fraction_done_filename>
+ <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:$PERL5LIB</setenv>
+ </task>
+ <unzip_input>
+ <zipfilename>ligands.zip</zipfilename>
+ </unzip_input>
+</job_desc>
diff --git a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
index 2691d09ea..a11f1fe9b 100644
--- a/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
+++ b/sci-biology/cmdock/files/cmdock-boinc-zip_job_0.1.2.xml
@@ -2,7 +2,8 @@
<task>
<application>/opt/cmdock-0.1.2/build/cmdock</application>
<stdout_filename>docking_log</stdout_filename>
- <command_line>-r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+ <command_line>-c -r target.prm -p /opt/cmdock-0.1.2/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+ <checkpoint_filename>docking_out.chk</checkpoint_filename>
<setenv>CMDOCK_ROOT=/opt/cmdock-0.1.2</setenv>
<setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.2/build:$LD_LIBRARY_PATH</setenv>
<setenv>PERL5LIB=/opt/cmdock-0.1.2/lib:$PERL5LIB</setenv>
diff --git a/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
new file mode 100644
index 000000000..6082dc8fe
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-boinc_job_0.1.3.xml
@@ -0,0 +1,10 @@
+<job_desc>
+ <task>
+ <application>/opt/cmdock-0.1.3/build/cmdock</application>
+ <stdout_filename>docking_log</stdout_filename>
+ <command_line>-r target.prm -p /opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+ <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.3</setenv>
+ <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv>
+ <setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv>
+ </task>
+</job_desc>
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/
@ 2021-07-22 8:29 Anna Vyalkova
0 siblings, 0 replies; 8+ messages in thread
From: Anna Vyalkova @ 2021-07-22 8:29 UTC (permalink / raw
To: gentoo-commits
commit: 4d7271caedd3ec77361bba7d98772767dfee8b78
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Mon Jul 19 10:55:37 2021 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Thu Jul 22 08:27:39 2021 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=4d7271ca
sci-biology/cmdock: make it prettier, fix perms
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.1.3.ebuild | 31 +++++++++++++++++-----
.../cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml | 10 +++----
sci-biology/cmdock/metadata.xml | 1 +
3 files changed, 30 insertions(+), 12 deletions(-)
diff --git a/sci-biology/cmdock/cmdock-0.1.3.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild
index e42b1f253..13e4bc2cc 100644
--- a/sci-biology/cmdock/cmdock-0.1.3.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.3.ebuild
@@ -10,7 +10,7 @@ DOCS_DIR="docs"
inherit python-any-r1 docs meson
DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
-HOMEPAGE="https://gitlab.com/Jukic/cmdock"
+HOMEPAGE="https://gitlab.com/Jukic/cmdock https://www.rxdock.org"
SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz"
S="${WORKDIR}/${PN}-v${PV}"
@@ -30,6 +30,8 @@ BDEPEND="
dev-libs/cxxopts
"
+MY_PREFIX="${EPREFIX}/opt/${P}"
+
src_prepare() {
default
rm -r include/indicators || die
@@ -38,7 +40,7 @@ src_prepare() {
src_configure() {
# very weird directory layout
local emesonargs=(
- --prefix="${EPREFIX}/opt/cmdock-${PV}"
+ --prefix="${MY_PREFIX}"
)
meson_src_configure
}
@@ -52,17 +54,32 @@ src_install() {
meson_src_install
if use boinc ; then
- insinto /var/lib/boinc/projects/www.sidock.si_sidock
- newins "${FILESDIR}/app_info_${PV}.xml" app_info.xml
- doins "${FILESDIR}/cmdock-boinc-zcp_job_${PV}.xml"
+ local project_root="/var/lib/boinc/projects/www.sidock.si_sidock"
+
+ local wrappers=( ${PN}-boinc-zcp )
+
+ insinto ${project_root}
+ insopts --owner boinc --group boinc
+
+ newins "${FILESDIR}"/app_info_${PV}.xml app_info.xml
+ touch "${ED}${project_root}"/docking_out.sd || die
+ fowners boinc:boinc ${project_root}/docking_out.sd
+
+ for app in "${wrappers[@]}" ; do
+ wrapperjob="${app}_job_${PV}.xml"
+ wrapperexe="${app}_wrapper_${PV}"
+
+ dosym -r /usr/bin/boinc-wrapper "${project_root}/${wrapperexe}"
- dosym -r /usr/bin/boinc-wrapper /var/lib/boinc/projects/www.sidock.si_sidock/cmdock-boinc-zcp_wrapper_${PV}
+ cp "${FILESDIR}"/${wrapperjob} "${S}" || die
+ sed "s:@PREFIX@:${MY_PREFIX}:g" -i ${wrapperjob} || die
+ doins ${wrapperjob}
+ done
fi
}
pkg_postinst() {
if use boinc ; then
- touch /var/lib/boinc/projects/www.sidock.si_sidock/docking_out.sd || die
elog
elog "The easiest way to do something useful with this application"
elog "is to attach it to SiDock@home BOINC project."
diff --git a/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
index 3c7818151..074bb29d4 100644
--- a/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
+++ b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
@@ -1,13 +1,13 @@
<job_desc>
<task>
- <application>/opt/cmdock-0.1.3/build/cmdock</application>
+ <application>@PREFIX@/build/cmdock</application>
<stdout_filename>docking_log</stdout_filename>
- <command_line>-c -j 1 -r target.prm -p /opt/cmdock-0.1.3/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
+ <command_line>-c -j 1 -r target.prm -p @PREFIX@/data/scripts/dock.prm -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
<checkpoint_filename>docking_out.chk</checkpoint_filename>
<fraction_done_filename>docking_out.progress</fraction_done_filename>
- <setenv>CMDOCK_ROOT=/opt/cmdock-0.1.3</setenv>
- <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.1.3/build:$LD_LIBRARY_PATH</setenv>
- <setenv>PERL5LIB=/opt/cmdock-0.1.3/lib:$PERL5LIB</setenv>
+ <setenv>CMDOCK_ROOT=@PREFIX@</setenv>
+ <setenv>LD_LIBRARY_PATH=@PREFIX@/build:$LD_LIBRARY_PATH</setenv>
+ <setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv>
</task>
<unzip_input>
<zipfilename>ligands.zip</zipfilename>
diff --git a/sci-biology/cmdock/metadata.xml b/sci-biology/cmdock/metadata.xml
index 9bb734387..f0cb44b3d 100644
--- a/sci-biology/cmdock/metadata.xml
+++ b/sci-biology/cmdock/metadata.xml
@@ -4,6 +4,7 @@
<upstream>
<remote-id type="gitlab">Jukic/cmdock</remote-id>
<bugs-to>https://gitlab.com/Jukic/cmdock/-/issues</bugs-to>
+ <doc>https://www.rxdock.org/api-documentation/devel/html</doc>
</upstream>
<maintainer type="person">
<email>cyber+gentoo@sysrq.in</email>
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/
@ 2021-11-25 7:16 Anna Vyalkova
0 siblings, 0 replies; 8+ messages in thread
From: Anna Vyalkova @ 2021-11-25 7:16 UTC (permalink / raw
To: gentoo-commits
commit: 50bb2e29704a88fb6d53a79ed4eda6a064d23c1a
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Thu Nov 25 07:15:21 2021 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Thu Nov 25 07:15:21 2021 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=50bb2e29
sci-biology/cmdock: add 0.1.4
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/Manifest | 1 +
sci-biology/cmdock/cmdock-0.1.3.ebuild | 90 ---------------------
sci-biology/cmdock/cmdock-0.1.4.ebuild | 94 ++++++++++++++++++++++
sci-biology/cmdock/files/app_info_0.1.4.xml | 37 +++++++++
.../cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml | 15 ++++
5 files changed, 147 insertions(+), 90 deletions(-)
diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
index 84968a8f8..cac8acdf0 100644
--- a/sci-biology/cmdock/Manifest
+++ b/sci-biology/cmdock/Manifest
@@ -1 +1,2 @@
DIST cmdock-v0.1.3.tar.gz 13416412 BLAKE2B abd6382943fb2ca2459fa493f8025e335821b96a95b88267dd493c28cd3280481b41ec6480fd3514cff126ab1077e89f075e5311393b1cd366403419e9c47454 SHA512 d941b672d14bad4fda4eaeb7aa313da1ade213241a1aee392747943a03afb6c66b3e93b8fd7eb9b1d8095b0632bd48cb062879cf445e3b54ce07069ad3087b22
+DIST cmdock-v0.1.4.tar.gz 14487352 BLAKE2B 3f212d596a12046f9a3b04376ca3e6d67f4391edba6f9c6e1fd372e7c7dbb23727ebd77787f125e57afca16e0cffc9b734dcdc7a83a825c52737218df371cbfd SHA512 6e1a366d82b311da0fdcd99ecf3e10962073453c7fdec9142854d472336f7f918bb76368b52e5904bf30e0aea6b8476a3ab522469daeaef52293ac481741b4bb
diff --git a/sci-biology/cmdock/cmdock-0.1.3.ebuild b/sci-biology/cmdock/cmdock-0.1.3.ebuild
deleted file mode 100644
index 13e4bc2cc..000000000
--- a/sci-biology/cmdock/cmdock-0.1.3.ebuild
+++ /dev/null
@@ -1,90 +0,0 @@
-# Copyright 2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..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 https://www.rxdock.org"
-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/${PV}"
-KEYWORDS="~amd64"
-IUSE="boinc"
-
-RDEPEND="
- dev-lang/perl
- boinc? ( sci-misc/boinc-wrapper )
-"
-BDEPEND="
- dev-cpp/eigen:3
- dev-cpp/indicators
- >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
- dev-libs/cxxopts
-"
-
-MY_PREFIX="${EPREFIX}/opt/${P}"
-
-src_prepare() {
- default
- rm -r include/indicators || die
-}
-
-src_configure() {
- # very weird directory layout
- local emesonargs=(
- --prefix="${MY_PREFIX}"
- )
- meson_src_configure
-}
-
-src_compile() {
- meson_src_compile
- docs_compile
-}
-
-src_install() {
- meson_src_install
-
- if use boinc ; then
- local project_root="/var/lib/boinc/projects/www.sidock.si_sidock"
-
- local wrappers=( ${PN}-boinc-zcp )
-
- insinto ${project_root}
- insopts --owner boinc --group boinc
-
- newins "${FILESDIR}"/app_info_${PV}.xml app_info.xml
- touch "${ED}${project_root}"/docking_out.sd || die
- fowners boinc:boinc ${project_root}/docking_out.sd
-
- for app in "${wrappers[@]}" ; do
- wrapperjob="${app}_job_${PV}.xml"
- wrapperexe="${app}_wrapper_${PV}"
-
- dosym -r /usr/bin/boinc-wrapper "${project_root}/${wrapperexe}"
-
- cp "${FILESDIR}"/${wrapperjob} "${S}" || die
- sed "s:@PREFIX@:${MY_PREFIX}:g" -i ${wrapperjob} || die
- doins ${wrapperjob}
- done
- fi
-}
-
-pkg_postinst() {
- if use boinc ; then
- elog
- elog "The easiest way to do something useful with this application"
- elog "is to attach it to SiDock@home BOINC project."
- elog
- elog "- Master URL: https://sidock.si/sidock/"
- elog "- Invitation code: Crunch_4Science"
- fi
-}
diff --git a/sci-biology/cmdock/cmdock-0.1.4.ebuild b/sci-biology/cmdock/cmdock-0.1.4.ebuild
new file mode 100644
index 000000000..70befcfcc
--- /dev/null
+++ b/sci-biology/cmdock/cmdock-0.1.4.ebuild
@@ -0,0 +1,94 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} pypy3 )
+
+BOINC_APP_OPTIONAL="true"
+
+DOCS_BUILDER="sphinx"
+DOCS_AUTODOC=0
+DOCS_DIR="docs"
+
+inherit python-any-r1 boinc-app docs flag-o-matic meson
+
+DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
+HOMEPAGE="https://gitlab.com/Jukic/cmdock https://www.rxdock.org"
+SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.gz"
+S="${WORKDIR}/${PN}-v${PV}"
+
+LICENSE="LGPL-3 ZLIB"
+SLOT="0/${PV}"
+KEYWORDS="~amd64"
+IUSE="apidoc boinc cpu_flags_x86_sse2"
+
+RDEPEND="
+ dev-lang/perl
+ boinc? ( sci-misc/boinc-wrapper )
+"
+BDEPEND="
+ dev-cpp/eigen:3
+ dev-cpp/indicators
+ >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
+ dev-libs/cxxopts
+ doc? ( app-doc/doxygen )
+"
+
+DOCS=( INSTALL.md README.md )
+
+BOINC_MASTER_URL="https://www.sidock.si/sidock/"
+BOINC_INVITATION_CODE="Crunch_4Science"
+BOINC_APP_HELPTEXT=\
+"The easiest way to do something useful with this application
+is to attach it to SiDock@home BOINC project."
+
+foreach_wrapper_job() {
+ sed -i "$1" \
+ -e "s:@PREFIX@:${EPREFIX}/opt/${P}:g" || die
+}
+
+src_configure() {
+ # very weird directory layout
+ local emesonargs=(
+ --prefix="${EPREFIX}/opt/${P}"
+ )
+ meson_src_configure
+
+ use cpu_flags_x86_sse2 || append-cppflags "-DBUNDLE_NO_SSE"
+}
+
+src_compile() {
+ meson_src_compile
+
+ # subshell prevents overriding global
+ # DOCS_BUILDER and DOCS_OUTDIR
+ (
+ DOCS_BUILDER="doxygen"
+ DOCS_OUTDIR="${S}/_build/html/api"
+ docs_compile
+ )
+ docs_compile
+}
+
+src_install() {
+ meson_src_install
+
+ if use boinc; then
+ doappinfo "${FILESDIR}"/app_info_${PV}.xml
+ dowrapper ${PN}-boinc-zcp
+
+ # install a blank file
+ insinto $(get_project_root)
+ insopts --owner boinc --group boinc
+ : newins - docking_out.sd
+ fi
+}
+
+pkg_postinst() {
+ use boinc && boinc-app_pkg_postinst
+}
+
+pkg_postrm() {
+ use boinc && boinc-app_pkg_postrm
+}
diff --git a/sci-biology/cmdock/files/app_info_0.1.4.xml b/sci-biology/cmdock/files/app_info_0.1.4.xml
new file mode 100644
index 000000000..85dcdb16a
--- /dev/null
+++ b/sci-biology/cmdock/files/app_info_0.1.4.xml
@@ -0,0 +1,37 @@
+<app_info>
+<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-boinc-zcp_wrapper_0.1.4</name>
+ <executable/>
+</file_info>
+
+<file_info>
+ <name>cmdock-boinc-zcp_job_0.1.4.xml</name>
+</file_info>
+<file_info>
+ <name>docking_out.sd</name>
+</file_info>
+
+<app_version>
+ <app_name>cmdock-boinc-zcp</app_name>
+ <version_num>200</version_num>
+ <file_ref>
+ <file_name>cmdock-boinc-zcp_wrapper_0.1.4</file_name>
+ <main_program/>
+ </file_ref>
+ <file_ref>
+ <file_name>cmdock-boinc-zcp_job_0.1.4.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-zcp_job_0.1.4.xml b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml
new file mode 100644
index 000000000..074bb29d4
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml
@@ -0,0 +1,15 @@
+<job_desc>
+ <task>
+ <application>@PREFIX@/build/cmdock</application>
+ <stdout_filename>docking_log</stdout_filename>
+ <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>
+ <checkpoint_filename>docking_out.chk</checkpoint_filename>
+ <fraction_done_filename>docking_out.progress</fraction_done_filename>
+ <setenv>CMDOCK_ROOT=@PREFIX@</setenv>
+ <setenv>LD_LIBRARY_PATH=@PREFIX@/build:$LD_LIBRARY_PATH</setenv>
+ <setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv>
+ </task>
+ <unzip_input>
+ <zipfilename>ligands.zip</zipfilename>
+ </unzip_input>
+</job_desc>
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/
@ 2022-06-02 4:55 Anna Vyalkova
0 siblings, 0 replies; 8+ messages in thread
From: Anna Vyalkova @ 2022-06-02 4:55 UTC (permalink / raw
To: gentoo-commits
commit: af0420fb5d5d6d99e31e9f0b8ff9f37033167c60
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Thu Jun 2 04:00:28 2022 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Thu Jun 2 04:54:15 2022 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=af0420fb
sci-biology/cmdock: fix CPU flags detection
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
.../{cmdock-0.1.4.ebuild => cmdock-0.1.4-r1.ebuild} | 8 +++++---
sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch | 15 +++++++++++++++
sci-biology/cmdock/metadata.xml | 2 +-
3 files changed, 21 insertions(+), 4 deletions(-)
diff --git a/sci-biology/cmdock/cmdock-0.1.4.ebuild b/sci-biology/cmdock/cmdock-0.1.4-r1.ebuild
similarity index 90%
rename from sci-biology/cmdock/cmdock-0.1.4.ebuild
rename to sci-biology/cmdock/cmdock-0.1.4-r1.ebuild
index 70befcfcc..cf79531ec 100644
--- a/sci-biology/cmdock/cmdock-0.1.4.ebuild
+++ b/sci-biology/cmdock/cmdock-0.1.4-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 2021 Gentoo Authors
+# Copyright 2021-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{8..10} pypy3 )
+PYTHON_COMPAT=( python3_{8..11} pypy3 )
BOINC_APP_OPTIONAL="true"
@@ -14,7 +14,7 @@ DOCS_DIR="docs"
inherit python-any-r1 boinc-app docs flag-o-matic meson
DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
-HOMEPAGE="https://gitlab.com/Jukic/cmdock https://www.rxdock.org"
+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}"
@@ -35,6 +35,8 @@ BDEPEND="
doc? ( app-doc/doxygen )
"
+PATCHES=( "${FILESDIR}"/cmdock-0.1.4-fix-detection.patch )
+
DOCS=( INSTALL.md README.md )
BOINC_MASTER_URL="https://www.sidock.si/sidock/"
diff --git a/sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch b/sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch
new file mode 100644
index 000000000..fceae1e5c
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch
@@ -0,0 +1,15 @@
+--- a/meson.build
++++ b/meson.build
+@@ -79,8 +79,10 @@
+
+ cpp_compiler = meson.get_compiler('cpp')
+
+-extended_encoders_available = (cpp_compiler.has_header('emmintrin.h') and
+- host_machine.cpu_family() == 'x86' and host_machine.cpu_family() == 'x86_64')
++extended_encoders_available = (
++ cpp_compiler.has_header('emmintrin.h') and
++ (host_machine.cpu_family() == 'x86' or host_machine.cpu_family() == 'x86_64')
++)
+
+ if not extended_encoders_available
+ add_project_arguments('-DBUNDLE_NO_SSE', language: 'cpp')
diff --git a/sci-biology/cmdock/metadata.xml b/sci-biology/cmdock/metadata.xml
index beddf8090..3f0fcb55e 100644
--- a/sci-biology/cmdock/metadata.xml
+++ b/sci-biology/cmdock/metadata.xml
@@ -4,7 +4,7 @@
<upstream>
<remote-id type="gitlab">Jukic/cmdock</remote-id>
<bugs-to>https://gitlab.com/Jukic/cmdock/-/issues</bugs-to>
- <doc>https://www.rxdock.org/documentation/devel/html</doc>
+ <doc>https://rxdock.gitlab.io/documentation/devel/html/</doc>
</upstream>
<maintainer type="person">
<email>cyber+gentoo@sysrq.in</email>
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/
@ 2022-12-12 11:44 Anna Vyalkova
0 siblings, 0 replies; 8+ messages in thread
From: Anna Vyalkova @ 2022-12-12 11:44 UTC (permalink / raw
To: gentoo-commits
commit: c7742604b7a71c99ce1d96cd72380c5021bb4613
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Mon Dec 12 11:41:07 2022 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Mon Dec 12 11:43:09 2022 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=c7742604
sci-biology/cmdock: drop 0.1.3-r1
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/Manifest | 1 -
sci-biology/cmdock/cmdock-0.1.3-r1.ebuild | 98 ----------------------
sci-biology/cmdock/files/app_info_0.1.3.xml | 37 --------
.../cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml | 15 ----
4 files changed, 151 deletions(-)
diff --git a/sci-biology/cmdock/Manifest b/sci-biology/cmdock/Manifest
index cac8acdf0..92078ebaa 100644
--- a/sci-biology/cmdock/Manifest
+++ b/sci-biology/cmdock/Manifest
@@ -1,2 +1 @@
-DIST cmdock-v0.1.3.tar.gz 13416412 BLAKE2B abd6382943fb2ca2459fa493f8025e335821b96a95b88267dd493c28cd3280481b41ec6480fd3514cff126ab1077e89f075e5311393b1cd366403419e9c47454 SHA512 d941b672d14bad4fda4eaeb7aa313da1ade213241a1aee392747943a03afb6c66b3e93b8fd7eb9b1d8095b0632bd48cb062879cf445e3b54ce07069ad3087b22
DIST cmdock-v0.1.4.tar.gz 14487352 BLAKE2B 3f212d596a12046f9a3b04376ca3e6d67f4391edba6f9c6e1fd372e7c7dbb23727ebd77787f125e57afca16e0cffc9b734dcdc7a83a825c52737218df371cbfd SHA512 6e1a366d82b311da0fdcd99ecf3e10962073453c7fdec9142854d472336f7f918bb76368b52e5904bf30e0aea6b8476a3ab522469daeaef52293ac481741b4bb
diff --git a/sci-biology/cmdock/cmdock-0.1.3-r1.ebuild b/sci-biology/cmdock/cmdock-0.1.3-r1.ebuild
deleted file mode 100644
index 099977f0a..000000000
--- a/sci-biology/cmdock/cmdock-0.1.3-r1.ebuild
+++ /dev/null
@@ -1,98 +0,0 @@
-# Copyright 2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} pypy3 )
-
-BOINC_APP_OPTIONAL="true"
-
-DOCS_BUILDER="sphinx"
-DOCS_AUTODOC=0
-DOCS_DIR="docs"
-
-inherit python-any-r1 boinc-app docs meson
-
-DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
-HOMEPAGE="https://gitlab.com/Jukic/cmdock https://www.rxdock.org"
-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="apidoc boinc"
-REQUIRED_USE="apidoc? ( doc )"
-
-RDEPEND="
- dev-lang/perl
- boinc? ( sci-misc/boinc-wrapper )
-"
-BDEPEND="
- dev-cpp/eigen:3
- dev-cpp/indicators
- >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
- dev-libs/cxxopts
- apidoc? ( app-doc/doxygen )
-"
-
-DOCS=( INSTALL.md README.md )
-
-BOINC_MASTER_URL="https://www.sidock.si/sidock/"
-BOINC_INVITATION_CODE="Crunch_4Science"
-BOINC_APP_HELPTEXT=\
-"The easiest way to do something useful with this application
-is to attach it to SiDock@home BOINC project."
-
-foreach_wrapper_job() {
- sed -i "$1" \
- -e "s:@PREFIX@:${EPREFIX}/opt/${P}:g" || die
-}
-
-src_prepare() {
- default
- rm -r include/indicators || die
-}
-
-src_configure() {
- # very weird directory layout
- local emesonargs=(
- --prefix="${EPREFIX}/opt/${P}"
- )
- meson_src_configure
-}
-
-src_compile() {
- meson_src_compile
-
- # subshell prevents from overriding global
- # DOCS_BUILDER and DOCS_OUTDIR
- use apidoc && (
- DOCS_BUILDER="doxygen"
- DOCS_OUTDIR="${S}/_build/html/api"
- docs_compile
- )
- docs_compile
-}
-
-src_install() {
- meson_src_install
-
- if use boinc; then
- doappinfo "${FILESDIR}"/app_info_${PV}.xml
- dowrapper ${PN}-boinc-zcp
-
- # install a blank file
- insinto $(get_project_root)
- insopts --owner boinc --group boinc
- : newins - docking_out.sd
- fi
-}
-
-pkg_postinst() {
- use boinc && boinc-app_pkg_postinst
-}
-
-pkg_postrm() {
- use boinc && boinc-app_pkg_postrm
-}
diff --git a/sci-biology/cmdock/files/app_info_0.1.3.xml b/sci-biology/cmdock/files/app_info_0.1.3.xml
deleted file mode 100644
index 162ad0c05..000000000
--- a/sci-biology/cmdock/files/app_info_0.1.3.xml
+++ /dev/null
@@ -1,37 +0,0 @@
-<app_info>
-<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-boinc-zcp_wrapper_0.1.3</name>
- <executable/>
-</file_info>
-
-<file_info>
- <name>cmdock-boinc-zcp_job_0.1.3.xml</name>
-</file_info>
-<file_info>
- <name>docking_out.sd</name>
-</file_info>
-
-<app_version>
- <app_name>cmdock-boinc-zcp</app_name>
- <version_num>100</version_num>
- <file_ref>
- <file_name>cmdock-boinc-zcp_wrapper_0.1.3</file_name>
- <main_program/>
- </file_ref>
- <file_ref>
- <file_name>cmdock-boinc-zcp_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-zcp_job_0.1.3.xml b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
deleted file mode 100644
index 074bb29d4..000000000
--- a/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.3.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<job_desc>
- <task>
- <application>@PREFIX@/build/cmdock</application>
- <stdout_filename>docking_log</stdout_filename>
- <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>
- <checkpoint_filename>docking_out.chk</checkpoint_filename>
- <fraction_done_filename>docking_out.progress</fraction_done_filename>
- <setenv>CMDOCK_ROOT=@PREFIX@</setenv>
- <setenv>LD_LIBRARY_PATH=@PREFIX@/build:$LD_LIBRARY_PATH</setenv>
- <setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv>
- </task>
- <unzip_input>
- <zipfilename>ligands.zip</zipfilename>
- </unzip_input>
-</job_desc>
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/
@ 2024-01-09 9:06 Anna Vyalkova
0 siblings, 0 replies; 8+ messages in thread
From: Anna Vyalkova @ 2024-01-09 9:06 UTC (permalink / raw
To: gentoo-commits
commit: aa759c4c98861c3b3e6b50cc154c76732930eb9f
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Tue Jan 9 09:05:39 2024 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Tue Jan 9 09:06:03 2024 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=aa759c4c
sci-biology/cmdock: drop *really* unused files
Closes: https://bugs.gentoo.org/921229
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.2.0.ebuild | 4 +--
sci-biology/cmdock/files/app_info_0.1.4.xml | 40 ----------------------
.../cmdock/files/cmdock-0.1.4-fix-detection.patch | 15 --------
.../cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml | 15 --------
4 files changed, 2 insertions(+), 72 deletions(-)
diff --git a/sci-biology/cmdock/cmdock-0.2.0.ebuild b/sci-biology/cmdock/cmdock-0.2.0.ebuild
index 66b5b8b5ef..c54bed6f98 100644
--- a/sci-biology/cmdock/cmdock-0.2.0.ebuild
+++ b/sci-biology/cmdock/cmdock-0.2.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 2021-2022 Gentoo Authors
+# Copyright 2021-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
BOINC_APP_OPTIONAL="true"
inherit boinc-app flag-o-matic meson optfeature python-any-r1
diff --git a/sci-biology/cmdock/files/app_info_0.1.4.xml b/sci-biology/cmdock/files/app_info_0.1.4.xml
deleted file mode 100644
index 923a7b9ac1..0000000000
--- a/sci-biology/cmdock/files/app_info_0.1.4.xml
+++ /dev/null
@@ -1,40 +0,0 @@
-<app_info>
-<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-boinc-zcp_wrapper_@PV@</name>
- <sticky/>
- <executable/>
-</file_info>
-
-<file_info>
- <name>cmdock-boinc-zcp_job_@PV@.xml</name>
- <sticky/>
-</file_info>
-<file_info>
- <name>docking_out.sd</name>
- <sticky/>
-</file_info>
-
-<app_version>
- <app_name>cmdock-boinc-zcp</app_name>
- <version_num>200</version_num>
- <file_ref>
- <file_name>cmdock-boinc-zcp_wrapper_@PV@</file_name>
- <main_program/>
- </file_ref>
- <file_ref>
- <file_name>cmdock-boinc-zcp_job_@PV@.xml</file_name>
- <open_name>job.xml</open_name>
- <copy_file/>
- </file_ref>
- <file_ref>
- <file_name>docking_out</file_name>
- <open_name>docking_out</open_name>
- <copy_file/>
- </file_ref>
-</app_version>
-</app_info>
diff --git a/sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch b/sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch
deleted file mode 100644
index fceae1e5cf..0000000000
--- a/sci-biology/cmdock/files/cmdock-0.1.4-fix-detection.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- a/meson.build
-+++ b/meson.build
-@@ -79,8 +79,10 @@
-
- cpp_compiler = meson.get_compiler('cpp')
-
--extended_encoders_available = (cpp_compiler.has_header('emmintrin.h') and
-- host_machine.cpu_family() == 'x86' and host_machine.cpu_family() == 'x86_64')
-+extended_encoders_available = (
-+ cpp_compiler.has_header('emmintrin.h') and
-+ (host_machine.cpu_family() == 'x86' or host_machine.cpu_family() == 'x86_64')
-+)
-
- if not extended_encoders_available
- add_project_arguments('-DBUNDLE_NO_SSE', language: 'cpp')
diff --git a/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml b/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml
deleted file mode 100644
index 074bb29d44..0000000000
--- a/sci-biology/cmdock/files/cmdock-boinc-zcp_job_0.1.4.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<job_desc>
- <task>
- <application>@PREFIX@/build/cmdock</application>
- <stdout_filename>docking_log</stdout_filename>
- <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>
- <checkpoint_filename>docking_out.chk</checkpoint_filename>
- <fraction_done_filename>docking_out.progress</fraction_done_filename>
- <setenv>CMDOCK_ROOT=@PREFIX@</setenv>
- <setenv>LD_LIBRARY_PATH=@PREFIX@/build:$LD_LIBRARY_PATH</setenv>
- <setenv>PERL5LIB=@PREFIX@/lib:$PERL5LIB</setenv>
- </task>
- <unzip_input>
- <zipfilename>ligands.zip</zipfilename>
- </unzip_input>
-</job_desc>
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/cmdock/, sci-biology/cmdock/files/
@ 2024-01-09 10:19 Anna Vyalkova
0 siblings, 0 replies; 8+ messages in thread
From: Anna Vyalkova @ 2024-01-09 10:19 UTC (permalink / raw
To: gentoo-commits
commit: bf5dd7c748cd41b6fa540780d668045d1836db0b
Author: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
AuthorDate: Tue Jan 9 10:19:33 2024 +0000
Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
CommitDate: Tue Jan 9 10:19:50 2024 +0000
URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=bf5dd7c7
sci-biology/cmdock: fix build
Closes: https://bugs.gentoo.org/901345
Signed-off-by: Anna (cybertailor) Vyalkova <cyber+gentoo <AT> sysrq.in>
sci-biology/cmdock/cmdock-0.2.0-r1.ebuild | 119 ++++++++++++++++++++
.../cmdock/files/cmdock-0.2.0-cxxopts.patch | 122 +++++++++++++++++++++
.../cmdock/files/cmdock-0.2.0-include.patch | 19 ++++
3 files changed, 260 insertions(+)
diff --git a/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild b/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
new file mode 100644
index 0000000000..e01a7ecf70
--- /dev/null
+++ b/sci-biology/cmdock/cmdock-0.2.0-r1.ebuild
@@ -0,0 +1,119 @@
+# Copyright 2021-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+BOINC_APP_OPTIONAL="true"
+inherit boinc-app flag-o-matic meson optfeature python-any-r1
+
+DESCRIPTION="Program for docking ligands to proteins and nucleic acids"
+HOMEPAGE="https://gitlab.com/Jukic/cmdock"
+SRC_URI="https://gitlab.com/Jukic/${PN}/-/archive/v${PV}/${PN}-v${PV}.tar.bz2"
+S="${WORKDIR}/${PN}-v${PV}"
+
+LICENSE="LGPL-3 ZLIB"
+SLOT="0/${PV}"
+KEYWORDS="~amd64"
+IUSE="apidoc boinc cpu_flags_x86_sse2 doc test"
+
+# Flaky tests
+RESTRICT="test"
+
+RDEPEND="
+ boinc? ( sci-misc/boinc-wrapper )
+"
+DEPEND="
+ dev-cpp/eigen:3
+ >=dev-cpp/indicators-2.3-r1
+ >=dev-cpp/pcg-cpp-0.98.1_p20210406-r1
+ >=dev-libs/cxxopts-3
+"
+BDEPEND="
+ apidoc? (
+ app-doc/doxygen
+ dev-texlive/texlive-fontutils
+ )
+ doc? (
+ $(python_gen_any_dep '
+ dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]
+ dev-python/sphinx[${PYTHON_USEDEP}]
+ ')
+ )
+ test? ( ${PYTHON_DEPS} )
+"
+
+PATCHES=(
+ "${FILESDIR}"/${P}-include.patch
+ "${FILESDIR}"/${P}-cxxopts.patch
+)
+
+DOCS=( README.md changelog.md )
+
+BOINC_MASTER_URL="https://www.sidock.si/sidock/"
+BOINC_INVITATION_CODE="Crunch_4Science"
+BOINC_APP_HELPTEXT=\
+"The easiest way to do something useful with this application
+is to attach it to SiDock@home BOINC project."
+
+INSTALL_PREFIX="${EPREFIX}/opt/${P}"
+
+python_check_deps() {
+ use doc || return 0
+
+ python_has_version "dev-python/sphinx[${PYTHON_USEDEP}]" &&
+ python_has_version "dev-python/insipid-sphinx-theme[${PYTHON_USEDEP}]"
+}
+
+foreach_wrapper_job() {
+ sed -e "s:@PREFIX@:${INSTALL_PREFIX}:g" -i "${1}" || die
+}
+
+src_prepare() {
+ default
+ python_fix_shebang "${S}"/bin
+}
+
+src_configure() {
+ # very weird directory layout
+ local emesonargs=(
+ --prefix="${INSTALL_PREFIX}"
+ $(meson_use apidoc)
+ $(meson_use doc)
+ $(meson_use test tests)
+ -Ddocdir="${EPREFIX}"/usr/share/doc/${PF}
+ )
+ meson_src_configure
+
+ use cpu_flags_x86_sse2 || append-cppflags "-DBUNDLE_NO_SSE"
+}
+
+src_install() {
+ meson_src_install
+ python_optimize "${D}${INSTALL_PREFIX}"/bin
+
+ if use boinc; then
+ doappinfo "${FILESDIR}"/app_info_${PV}.xml
+ dowrapper cmdock-l
+
+ # install cmdock executable
+ exeinto "$(get_project_root)"
+ exeopts --owner root --group boinc
+ newexe "${D}${INSTALL_PREFIX}"/bin/cmdock cmdock-${PV}
+
+ # install a blank file
+ touch "${T}"/docking_out || die
+ insinto "$(get_project_root)"
+ insopts --owner root --group boinc
+ doins "${T}"/docking_out
+ fi
+}
+
+pkg_postinst() {
+ optfeature "sdtether.py and sdrmsd.py scripts" "dev-python/numpy sci-chemistry/openbabel[python]"
+ use boinc && boinc-app_pkg_postinst
+}
+
+pkg_postrm() {
+ use boinc && boinc-app_pkg_postrm
+}
diff --git a/sci-biology/cmdock/files/cmdock-0.2.0-cxxopts.patch b/sci-biology/cmdock/files/cmdock-0.2.0-cxxopts.patch
new file mode 100644
index 0000000000..4d7f227957
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-0.2.0-cxxopts.patch
@@ -0,0 +1,122 @@
+Update to cxxopts 3.0
+
+--- a/meson.build
++++ b/meson.build
+@@ -40,7 +40,7 @@ if cpp_compiler.get_id() == 'msvc'
+ message('Applying workaround for MSVC by adding flag /Zc:twoPhase-: https://stackoverflow.com/questions/56782470/why-do-i-have-warning-c4199-two-phase-name-lookup-is-not-supported-for-c-cli')
+ endif
+
+-cxxopts_dep = dependency('cxxopts', fallback : ['cxxopts', 'cxxopts_dep'])
++cxxopts_dep = dependency('cxxopts', version : '>=3.0', fallback : ['cxxopts', 'cxxopts_dep'])
+ eigen3_dep = dependency('eigen3', fallback : ['eigen', 'eigen_dep'])
+ openmp_dep = dependency('openmp', required : false)
+
+diff --git a/src/exe/cmcavity.cxx b/src/exe/cmcavity.cxx
+index 427d3c0..3a5c747 100644
+--- a/src/exe/cmcavity.cxx
++++ b/src/exe/cmcavity.cxx
+@@ -41,7 +41,7 @@ void PrintHeaderAddon(std::ostream &outputStream) {
+ // MAIN PROGRAM STARTS HERE
+ /////////////////////////////////////////////////////////////////////
+
+-int main(int argc, char *argv[]) {
++int main(const int argc, const char *argv[]) {
+ // Handle obsolete arguments, if any
+ for (int i = 0; i < argc; i++) {
+ std::string opt = argv[i];
+@@ -451,7 +451,7 @@ int main(int argc, char *argv[]) {
+
+ logFile.close();
+ }
+- } catch (const cxxopts::OptionException &e) {
++ } catch (const cxxopts::exceptions::exception &e) {
+ std::cout << "Error parsing options: " << e.what() << std::endl;
+ return 1;
+ } catch (RbtError &e) {
+@@ -463,4 +463,4 @@ int main(int argc, char *argv[]) {
+ _RBTOBJECTCOUNTER_DUMP_(std::cout)
+
+ return 0;
+-}
+\ No newline at end of file
++}
+diff --git a/src/exe/cmdock.cxx b/src/exe/cmdock.cxx
+index 10e18ca..86bbff1 100644
+--- a/src/exe/cmdock.cxx
++++ b/src/exe/cmdock.cxx
+@@ -80,7 +80,7 @@ void printHelpFooter() {
+ // MAIN PROGRAM STARTS HERE
+ /////////////////////////////////////////////////////////////////////
+
+-int main(int argc, char *argv[]) {
++int main(const int argc, const char *argv[]) {
+ // Handle premature termination
+ signal (SIGINT, terminator);
+
+@@ -941,7 +941,7 @@ int main(int argc, char *argv[]) {
+ log << "Thank you for using " << Rbt::GetProgramName() << " "
+ << Rbt::GetVersion() << "." << std::endl;
+ logFile.close();
+- } catch (const cxxopts::OptionException &e) {
++ } catch (const cxxopts::exceptions::exception &e) {
+ std::cout << "Error parsing options: " << e.what() << std::endl;
+ return 1;
+ } catch (RbtError &e) {
+@@ -953,4 +953,4 @@ int main(int argc, char *argv[]) {
+ _RBTOBJECTCOUNTER_DUMP_(std::cout)
+
+ return 0;
+-}
+\ No newline at end of file
++}
+diff --git a/src/exe/cmmoegrid.cxx b/src/exe/cmmoegrid.cxx
+index 4bff8f3..bf74b52 100644
+--- a/src/exe/cmmoegrid.cxx
++++ b/src/exe/cmmoegrid.cxx
+@@ -57,7 +57,7 @@ RbtModelList CreateProbes(std::string anAtomTypeStr) {
+ // MAIN PROGRAM STARTS HERE
+ /////////////////////////////////////////////////////////////////////
+
+-int main(int argc, char *argv[]) {
++int main(const int argc, const char *argv[]) {
+ std::cout.setf(std::ios_base::left, std::ios_base::adjustfield);
+
+ // Strip off the path to the executable, leaving just the file name
+@@ -268,7 +268,7 @@ int main(int argc, char *argv[]) {
+ }
+ std::cout << "done." << std::endl;
+ }
+- } catch (const cxxopts::OptionException &e) {
++ } catch (const cxxopts::exceptions::exception &e) {
+ std::cout << "Error parsing options: " << e.what() << std::endl;
+ return 1;
+ } catch (RbtError &e) {
+diff --git a/src/exe/cmzip.cxx b/src/exe/cmzip.cxx
+index 1d1f69a..043d7be 100644
+--- a/src/exe/cmzip.cxx
++++ b/src/exe/cmzip.cxx
+@@ -504,7 +504,7 @@ void rescue(cxxopts::ParseResult result){
+ }
+
+ // ENTRY POINT
+-int main(int argc, char *argv[]) {
++int main(const int argc, const char *argv[]) {
+ // Handle premature termination
+ signal (SIGINT, terminator);
+
+@@ -580,7 +580,7 @@ Use this if CmDock terminates prematurely. CmZIP will search for records in the
+ return 0;
+ }
+
+- } catch (const cxxopts::OptionException &e) {
++ } catch (const cxxopts::exceptions::exception &e) {
+ std::cout << "Error parsing options: " << e.what() << std::endl;
+ return 1;
+ } catch (const std::exception &exc) {
+@@ -589,4 +589,4 @@ Use this if CmDock terminates prematurely. CmZIP will search for records in the
+ /*} catch (...) {
+ std::cout << "Unknown exception" << std::endl;
+ }*/
+-}
+\ No newline at end of file
++}
diff --git a/sci-biology/cmdock/files/cmdock-0.2.0-include.patch b/sci-biology/cmdock/files/cmdock-0.2.0-include.patch
new file mode 100644
index 0000000000..b4a6e80bb0
--- /dev/null
+++ b/sci-biology/cmdock/files/cmdock-0.2.0-include.patch
@@ -0,0 +1,19 @@
+Rbt.cxx: Add missing include
+
+--- a/src/lib/Rbt.cxx
++++ b/src/lib/Rbt.cxx
+@@ -15,6 +15,7 @@
+ #include <algorithm> //For sort
+ #include <climits> //For PATH_MAX
+ #include <cstdlib> //For getenv
++#include <cstdint> //For int types
+ #include <ctime> //For time functions
+ #include <dirent.h> //For directory handling
+ #include <fstream> //For ifstream
+@@ -581,4 +582,4 @@ bool Rbt::endsWith (std::string const &fullString, std::string const &ending) {
+ } else {
+ return false;
+ }
+-}
+\ No newline at end of file
++}
^ permalink raw reply related [flat|nested] 8+ messages in thread
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