[gentoo-commits] proj/sci:master commit in: sci-biology/RAILS/
commit: 4a5df3568fcb228f465287849d51a18cea1bc76a
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Thu Jan 2 08:36:48 2020 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jan 2 08:36:48 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4a5df356
sci-biology/RAILS: version bump
The minimap2-based wrapper script won't work as we do not have minimap2
in Gentoo Linux yet.
Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
.../RAILS/{RAILS-1.4.1.ebuild => RAILS-1.5.1.ebuild} | 14 +-
1 file changed, 9 insertions(+), 5 deletions(-)
diff --git a/sci-biology/RAILS/RAILS-1.4.1.ebuild
b/sci-biology/RAILS/RAILS-1.5.1.ebuild
similarity index 54%
rename from sci-biology/RAILS/RAILS-1.4.1.ebuild
rename to sci-biology/RAILS/RAILS-1.5.1.ebuild
index 9360c6040..df5f0ea4a 100644
--- a/sci-biology/RAILS/RAILS-1.4.1.ebuild
+++ b/sci-biology/RAILS/RAILS-1.5.1.ebuild
@@ -1,11 +1,11 @@
-# Copyright 2018 Gentoo Authors
+# Copyright 2018-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-DESCRIPTION="Cobbler and RAILS scaffolding tools"
+DESCRIPTION="Cobbler and RAILS scaffolding tools acting on SAM streams"
HOMEPAGE="https://github.com/bcgsc/RAILS";
-SRC_URI="https://github.com/bcgsc/RAILS/archive/v1.4.1.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/bcgsc/RAILS/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3+"
SLOT="0"
@@ -15,12 +15,16 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
dev-lang/perl
- sci-biology/samtools"
+ sci-biology/samtools
+ sci-biology/bwa
+"
+# bin/runRAILSminimap.sh calls minimap2 but one can stream the SAM data
directly
BDEPEND=""
src_prepare(){
# remove hardcoded PATHs
- sed -e 's@^\.\./@@g' -e 's@^export PATH=/gsc/btl/linuxbrew@#&1@' -i
bin/runRAILS.sh || die
+ # https://github.com/bcgsc/RAILS/issues/8
+ sed -e 's@^\.\./@@g' -e 's@^export PATH=/gsc/btl/linuxbrew@#&1@' -i
bin/*.sh || die
default
}
[gentoo-commits] proj/sci:master commit in: sci-biology/RAILS/
commit: 3241a12426e95464547ee45cc6489df6fd8a4350
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Thu Dec 6 15:33:03 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Dec 6 15:33:03 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3241a124
sci-biology/RAILS: new package for (re-)scaffolding
This is a successor of SSAKE and of LINKS scaffolders.
Remove hardcoded PATHs, see
https://github.com/bcgsc/RAILS/issues/8#issuecomment-444898365
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/RAILS/RAILS-1.4.1.ebuild | 30 ++
sci-biology/RAILS/metadata.xml | 12
2 files changed, 42 insertions(+)
diff --git a/sci-biology/RAILS/RAILS-1.4.1.ebuild
b/sci-biology/RAILS/RAILS-1.4.1.ebuild
new file mode 100644
index 0..9360c6040
--- /dev/null
+++ b/sci-biology/RAILS/RAILS-1.4.1.ebuild
@@ -0,0 +1,30 @@
+# Copyright 2018 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Cobbler and RAILS scaffolding tools"
+HOMEPAGE="https://github.com/bcgsc/RAILS";
+SRC_URI="https://github.com/bcgsc/RAILS/archive/v1.4.1.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ dev-lang/perl
+ sci-biology/samtools"
+BDEPEND=""
+
+src_prepare(){
+ # remove hardcoded PATHs
+ sed -e 's@^\.\./@@g' -e 's@^export PATH=/gsc/btl/linuxbrew@#&1@' -i
bin/runRAILS.sh || die
+ default
+}
+
+src_install(){
+ dobin bin/*
+ dodoc readme.md paper/paper.pdf
+}
diff --git a/sci-biology/RAILS/metadata.xml b/sci-biology/RAILS/metadata.xml
new file mode 100644
index 0..138cb7705
--- /dev/null
+++ b/sci-biology/RAILS/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
+
+
