From 4a5df3568fcb228f465287849d51a18cea1bc76a Mon Sep 17 00:00:00 2001
From: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Date: Thu, 2 Jan 2020 09:36:48 +0100
Subject: 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@fold.natur.cuni.cz>
---
 sci-biology/RAILS/Manifest           |  2 +-
 sci-biology/RAILS/RAILS-1.4.1.ebuild | 30 ------------------------------
 sci-biology/RAILS/RAILS-1.5.1.ebuild | 34 ++++++++++++++++++++++++++++++++++
 3 files changed, 35 insertions(+), 31 deletions(-)
 delete mode 100644 sci-biology/RAILS/RAILS-1.4.1.ebuild
 create mode 100644 sci-biology/RAILS/RAILS-1.5.1.ebuild

diff --git a/sci-biology/RAILS/Manifest b/sci-biology/RAILS/Manifest
index f31fe08bc..d9f432dff 100644
--- a/sci-biology/RAILS/Manifest
+++ b/sci-biology/RAILS/Manifest
@@ -1 +1 @@
-DIST RAILS-1.4.1.tar.gz 758732 BLAKE2B e2ec3b06a00dddf87220f3f492a274e7a9dd80a35c93d5326c5baf8f8281729d36444f4af0ae246429b4ac4182ceed8cd16ff877d9b07970b733e1cea17e1a6d SHA512 eb44b25ed7237fc38cba3d435c76ac813385fe2e6906144103279888107102fb30d280a4ff2256ae744291d769aba5d87125c77c348fb7300dcbd319520450fd
+DIST RAILS-1.5.1.tar.gz 1100024 BLAKE2B 64938481a333a1e9cb54798540327413f5dc95be38f4b5a88fc4bc38f31ab889da19804f9470bc90f63c690342acecb9907c12cb68e7f359d7cd8885fb6248e6 SHA512 37b6c4d35858c0b41a9ca04076a360aa732a12ab0f9bfa170aa307b2c7bbe28b6ba7b2f5b9f3ba949036fb274c96c934ad34e675b468608a8580cf3fdb7dba32
diff --git a/sci-biology/RAILS/RAILS-1.4.1.ebuild b/sci-biology/RAILS/RAILS-1.4.1.ebuild
deleted file mode 100644
index 9360c6040..000000000
--- a/sci-biology/RAILS/RAILS-1.4.1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# 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/RAILS-1.5.1.ebuild b/sci-biology/RAILS/RAILS-1.5.1.ebuild
new file mode 100644
index 000000000..df5f0ea4a
--- /dev/null
+++ b/sci-biology/RAILS/RAILS-1.5.1.ebuild
@@ -0,0 +1,34 @@
+# Copyright 2018-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Cobbler and RAILS scaffolding tools acting on SAM streams"
+HOMEPAGE="https://github.com/bcgsc/RAILS"
+SRC_URI="https://github.com/bcgsc/RAILS/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	dev-lang/perl
+	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
+	# https://github.com/bcgsc/RAILS/issues/8
+	sed -e 's@^\.\./@@g' -e 's@^export PATH=/gsc/btl/linuxbrew@#&1@' -i bin/*.sh || die
+	default
+}
+
+src_install(){
+	dobin bin/*
+	dodoc readme.md paper/paper.pdf
+}
-- 
cgit v1.2.3-65-gdbad