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| author |   Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2020-01-02 09:36:48 +0100 |
|---|---|---|
| committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2020-01-02 09:36:48 +0100 |
| commit | 4a5df3568fcb228f465287849d51a18cea1bc76a (patch) | |
| tree | e491895f9af52feb829b6ec848c64224d99c9690 | |
| parent | sci-libs/libmaus2: point to libmaus2 and to gitlab (diff) | |
| download | sci-4a5df356.tar.gz sci-4a5df356.tar.bz2 sci-4a5df356.zip | |
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>
| -rw-r--r-- | sci-biology/RAILS/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/RAILS/RAILS-1.5.1.ebuild (renamed from sci-biology/RAILS/RAILS-1.4.1.ebuild) | 14 |
2 files changed, 10 insertions, 6 deletions
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-1.5.1.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 } |