* [gentoo-commits] proj/sci:master commit in: sci-biology/LINKS/
@ 2021-11-29 11:41 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2021-11-29 11:41 UTC (permalink / raw
To: gentoo-commits
commit: 5db6563203432be7454b285bba50fc79daaac21d
Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Mon Nov 29 11:41:16 2021 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Nov 29 11:41:16 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5db65632
sci-biology/LINKS: remove keywords
This package is supposed to be executed from within compiled
source tree. See comments in the ebuild what needs to be fixed.
https://github.com/bcgsc/LINKS/pull/59
https://github.com/bcgsc/LINKS/issues/31
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>
sci-biology/LINKS/LINKS-1.8.7.ebuild | 31 ++++++++++++++++++++++++++++---
1 file changed, 28 insertions(+), 3 deletions(-)
diff --git a/sci-biology/LINKS/LINKS-1.8.7.ebuild b/sci-biology/LINKS/LINKS-1.8.7.ebuild
index 5009e9922..898898b94 100644
--- a/sci-biology/LINKS/LINKS-1.8.7.ebuild
+++ b/sci-biology/LINKS/LINKS-1.8.7.ebuild
@@ -9,17 +9,42 @@ SRC_URI="https://github.com/bcgsc/LINKS/archive/refs/tags/v${PV}.tar.gz -> ${P}.
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
RESTRICT="test"
RDEPEND="
>=dev-lang/perl-1.6
dev-lang/swig
- sci-biology/btl_bloomfilter
+ dev-util/cppcheck
"
+# sci-biology/btl_bloomfilter
+
+src_compile(){
+ cd btllib | die "Cannot chdir to bundled btllib/"
+ ./compile-wrappers || die "Failed to compile bundled btllib"
+ # baah, this also does some kind of install
+ # SUCCESS: sdsl was installed successfully!
+ # The sdsl include files are located in $foo'/LINKS/btllib/external/sdsl-lite/installdir/include'.
+ # The library files are located in $foo'/LINKS/btllib/external/sdsl-lite/installdir/lib'.
+ #
+ # Sample programs can be found in the examples-directory.
+ # A program 'example.cpp' can be compiled with the command:
+ # g++ -std=c++11 -DNDEBUG -O3 [-msse4.2] \
+ # -I$foo/LINKS/btllib/external/sdsl-lite/installdir/include -L$foo/LINKS/btllib/external/sdsl-lite/installdir/lib \
+ # example.cpp -lsdsl -ldivsufsort -ldivsufsort64
+ #
+ # Tests in the test-directory
+ # A cheat sheet in the extras/cheatsheet-directory.
+ # Have fun!
+ # [2/3] Installing files.
+ # Installing extras/python/_btllib.so to $foo/LINKS/btllib/python
+ # Installing $foo/LINKS/btllib/extras/python/btllib.py to $foo/LINKS/btllib/python
+}
src_install(){
- dobin bin/LINKS *.pl releases/links_v1.8.5/tools/*.pl
+ sed -e 's#$(bin)/../src/##' -i bin/LINKS-make || die
+ sed -e 's#perl $(bin)/##' -i bin/LINKS-make || die
+ dobin bin/LINKS bin/LINKS-make src/LINKS_CPP bin/*.pl tools/*.pl
dodoc README.md
}
^ permalink raw reply related [flat|nested] 5+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/LINKS/
@ 2022-01-25 19:15 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 19:15 UTC (permalink / raw
To: gentoo-commits
commit: 52f4c2c9ae553f0094fc30b52b349dca5ae13abd
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 17:14:40 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 17:14:40 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=52f4c2c9
sci-biology/LINKS: fix dep on swig
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/LINKS/LINKS-2.0.1.ebuild | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/sci-biology/LINKS/LINKS-2.0.1.ebuild b/sci-biology/LINKS/LINKS-2.0.1.ebuild
index 75d50a1b0..c1c9cc5d8 100644
--- a/sci-biology/LINKS/LINKS-2.0.1.ebuild
+++ b/sci-biology/LINKS/LINKS-2.0.1.ebuild
@@ -14,7 +14,8 @@ KEYWORDS="~amd64"
RDEPEND="
>=dev-lang/perl-1.6
- dev-lang/swig
dev-util/cppcheck
"
-DEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}
+ dev-lang/swig
+"
^ permalink raw reply related [flat|nested] 5+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/LINKS/
@ 2022-01-25 13:32 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 13:32 UTC (permalink / raw
To: gentoo-commits
commit: 58a63be80af5b547d2f6ceaa6377a84365ccfe41
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 13:28:59 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 13:28:59 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=58a63be8
sci-biology/LINKS: bump to 2.0.1
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/LINKS/LINKS-1.8.7.ebuild | 50 ------------------------------------
sci-biology/LINKS/LINKS-2.0.1.ebuild | 20 +++++++++++++++
2 files changed, 20 insertions(+), 50 deletions(-)
diff --git a/sci-biology/LINKS/LINKS-1.8.7.ebuild b/sci-biology/LINKS/LINKS-1.8.7.ebuild
deleted file mode 100644
index 898898b94..000000000
--- a/sci-biology/LINKS/LINKS-1.8.7.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads"
-HOMEPAGE="https://github.com/bcgsc/LINKS"
-SRC_URI="https://github.com/bcgsc/LINKS/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-
-RESTRICT="test"
-
-RDEPEND="
- >=dev-lang/perl-1.6
- dev-lang/swig
- dev-util/cppcheck
-"
-# sci-biology/btl_bloomfilter
-
-src_compile(){
- cd btllib | die "Cannot chdir to bundled btllib/"
- ./compile-wrappers || die "Failed to compile bundled btllib"
- # baah, this also does some kind of install
- # SUCCESS: sdsl was installed successfully!
- # The sdsl include files are located in $foo'/LINKS/btllib/external/sdsl-lite/installdir/include'.
- # The library files are located in $foo'/LINKS/btllib/external/sdsl-lite/installdir/lib'.
- #
- # Sample programs can be found in the examples-directory.
- # A program 'example.cpp' can be compiled with the command:
- # g++ -std=c++11 -DNDEBUG -O3 [-msse4.2] \
- # -I$foo/LINKS/btllib/external/sdsl-lite/installdir/include -L$foo/LINKS/btllib/external/sdsl-lite/installdir/lib \
- # example.cpp -lsdsl -ldivsufsort -ldivsufsort64
- #
- # Tests in the test-directory
- # A cheat sheet in the extras/cheatsheet-directory.
- # Have fun!
- # [2/3] Installing files.
- # Installing extras/python/_btllib.so to $foo/LINKS/btllib/python
- # Installing $foo/LINKS/btllib/extras/python/btllib.py to $foo/LINKS/btllib/python
-}
-
-src_install(){
- sed -e 's#$(bin)/../src/##' -i bin/LINKS-make || die
- sed -e 's#perl $(bin)/##' -i bin/LINKS-make || die
- dobin bin/LINKS bin/LINKS-make src/LINKS_CPP bin/*.pl tools/*.pl
- dodoc README.md
-}
diff --git a/sci-biology/LINKS/LINKS-2.0.1.ebuild b/sci-biology/LINKS/LINKS-2.0.1.ebuild
new file mode 100644
index 000000000..75d50a1b0
--- /dev/null
+++ b/sci-biology/LINKS/LINKS-2.0.1.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads"
+HOMEPAGE="https://github.com/bcgsc/LINKS"
+SRC_URI="https://github.com/bcgsc/LINKS/releases/download/v${PV}/links-v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/links-${PV}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-lang/perl-1.6
+ dev-lang/swig
+ dev-util/cppcheck
+"
+DEPEND="${RDEPEND}"
^ permalink raw reply related [flat|nested] 5+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/LINKS/
@ 2021-10-17 15:56 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2021-10-17 15:56 UTC (permalink / raw
To: gentoo-commits
commit: 377d1d836ceacf807b6c0eec677a841eb8d45c2c
Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Sun Oct 17 15:56:52 2021 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Oct 17 15:56:52 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=377d1d83
sci-biology/LINKS: install the tools/*.pl files from archive
... until https://github.com/bcgsc/LINKS/issues/31 is fixed.
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>
sci-biology/LINKS/LINKS-1.8.7.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/LINKS/LINKS-1.8.7.ebuild b/sci-biology/LINKS/LINKS-1.8.7.ebuild
index e9cf2fbd8..5009e9922 100644
--- a/sci-biology/LINKS/LINKS-1.8.7.ebuild
+++ b/sci-biology/LINKS/LINKS-1.8.7.ebuild
@@ -20,6 +20,6 @@ RDEPEND="
"
src_install(){
- dobin bin/LINKS *.pl tools/*.pl
+ dobin bin/LINKS *.pl releases/links_v1.8.5/tools/*.pl
dodoc README.md
}
^ permalink raw reply related [flat|nested] 5+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/LINKS/
@ 2021-10-17 15:42 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2021-10-17 15:42 UTC (permalink / raw
To: gentoo-commits
commit: f4a311c42b306a1a49fa91c28203f388d324d326
Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Sun Oct 17 15:42:43 2021 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Oct 17 15:42:43 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f4a311c4
sci-biology/LINKS: new package
The LINKS perl script probably needs some sed hackery to eventually
start using system-wide btl_bloomfilter file BloomFilter.i and also
perl's CORE/EXTERN.h.
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>
sci-biology/LINKS/LINKS-1.8.7.ebuild | 25 +++++++++++++++++++++++++
sci-biology/LINKS/metadata.xml | 12 ++++++++++++
2 files changed, 37 insertions(+)
diff --git a/sci-biology/LINKS/LINKS-1.8.7.ebuild b/sci-biology/LINKS/LINKS-1.8.7.ebuild
new file mode 100644
index 000000000..e9cf2fbd8
--- /dev/null
+++ b/sci-biology/LINKS/LINKS-1.8.7.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads"
+HOMEPAGE="https://github.com/bcgsc/LINKS"
+SRC_URI="https://github.com/bcgsc/LINKS/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RESTRICT="test"
+
+RDEPEND="
+ >=dev-lang/perl-1.6
+ dev-lang/swig
+ sci-biology/btl_bloomfilter
+"
+
+src_install(){
+ dobin bin/LINKS *.pl tools/*.pl
+ dodoc README.md
+}
diff --git a/sci-biology/LINKS/metadata.xml b/sci-biology/LINKS/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/LINKS/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
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