[gentoo-commits] proj/sci:master commit in: sci-biology/RAILS/

[gentoo-commits] proj/sci:master commit in: sci-biology/RAILS/

[Martin Mokrejs]

commit:     3241a12426e95464547ee45cc6489df6fd8a4350
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Dec  6 15:33:03 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Dec  6 15:33:03 2018 +0000
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 <mmokrejs <AT> 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 000000000..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 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/RAILS/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>

[gentoo-commits] proj/sci:master commit in: sci-biology/RAILS/

[Martin Mokrejs]

commit:     4a5df3568fcb228f465287849d51a18cea1bc76a
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan  2 08:36:48 2020 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan  2 08:36:48 2020 +0000
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 <mmokrejs <AT> 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
 }