[gentoo-commits] proj/sci:master commit in: sci-biology/LINKS/
commit: 52f4c2c9ae553f0094fc30b52b349dca5ae13abd Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Jan 25 17:14:40 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Jan 25 17:14:40 2022 + 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 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 +"
[gentoo-commits] proj/sci:master commit in: sci-biology/LINKS/
commit: 58a63be80af5b547d2f6ceaa6377a84365ccfe41 Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Jan 25 13:28:59 2022 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Jan 25 13:28:59 2022 + 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 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..0 --- 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 $(bin)/##' -i bin/LINKS-make || die - dobin bin/LINKS bin/LINKS-make src/LINKS_CPP bin/*.pl tools/*.pl - dodoc README.md -} diff --git a/sci-biology/LINKS/LINKS-2.0.1.ebuild b/sci-biology/LINKS/LINKS-2.0.1.ebuild new file mode 100644 index 0..75d50a1b0 --- /dev/null +++ b/sci-biology/LINKS/LINKS-2.0.1.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads" +HOMEPAGE="https://github.com/bcgsc/LINKS"; +SRC_URI="https://github.com/bcgsc/LINKS/releases/download/v${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}"
[gentoo-commits] proj/sci:master commit in: sci-biology/LINKS/
commit: 5db6563203432be7454b285bba50fc79daaac21d Author: Martin Mokrejs gmail com> AuthorDate: Mon Nov 29 11:41:16 2021 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Nov 29 11:41:16 2021 + 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 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 }
[gentoo-commits] proj/sci:master commit in: sci-biology/LINKS/
commit: 377d1d836ceacf807b6c0eec677a841eb8d45c2c Author: Martin Mokrejs gmail com> AuthorDate: Sun Oct 17 15:56:52 2021 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Oct 17 15:56:52 2021 + 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 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 }
[gentoo-commits] proj/sci:master commit in: sci-biology/LINKS/
commit: f4a311c42b306a1a49fa91c28203f388d324d326 Author: Martin Mokrejs gmail com> AuthorDate: Sun Oct 17 15:42:43 2021 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Oct 17 15:42:43 2021 + 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 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 0..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 0..138cb7705 --- /dev/null +++ b/sci-biology/LINKS/metadata.xml @@ -0,0 +1,12 @@ + +http://www.gentoo.org/dtd/metadata.dtd";> + + + mmokr...@fold.natur.cuni.cz + Martin Mokrejs + + + sci-biol...@gentoo.org + Gentoo Biology Project + +