[Gsrc-commit] trunk r5666: update bowtie2 to 2.3.4.1

[Carl Hansen]

------------------------------------------------------------
revno: 5666
revision-id: address@hidden
parent: address@hidden
committer: address@hidden
branch nick: trunk
timestamp: Fri 2018-06-29 23:49:39 -0700
message:
  update bowtie2 to 2.3.4.1
renamed:
  pkg/bio/bowtie/ => pkg/bio/bowtie2/ bowtie-20160617195624-kwz1a09vkg4le6fu-8
modified:
  pkg/bio/bowtie2/Makefile       makefile-20160617195624-kwz1a09vkg4le6fu-79
  pkg/bio/bowtie2/sha256sums     sha256sums-20160617195624-kwz1a09vkg4le6fu-80

=== renamed directory 'pkg/bio/bowtie' => 'pkg/bio/bowtie2'
=== modified file 'pkg/bio/bowtie2/Makefile'
--- a/pkg/bio/bowtie/Makefile   2016-06-17 19:57:40 +0000
+++ b/pkg/bio/bowtie2/Makefile  2018-06-30 06:49:39 +0000
@@ -1,13 +1,14 @@
 # Copyright © 2014 Brandon Invergo <address@hidden>
-#
-# This file is part of BioSRC.
-#
-# BioSRC is free software: you can redistribute it and/or modify it
+# Copyright © 2018 Carl Hansen <address@hidden>
+#
+# This file is part of BioSRC and GSRC.
+#
+# GSRC is free software: you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 #
-# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
 # or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public
 # License for more details.
@@ -15,10 +16,9 @@
 # You should have received a copy of the GNU General Public License
 # along with BioSRC.  If not, see <http://www.gnu.org/licenses/>.
 
-NAME = Bowtie 2
-GARNAME = bowtie
-UPSTREAMNAME = bowtie2
-GARVERSION = 2.2.4
+NAME = Bowtie2
+GARNAME = bowtie2
+GARVERSION = 2.3.4.1
 HOME_URL = http://bowtie-bio.sourceforge.net/bowtie2
 DESCRIPTION = Fast and sensitive read alignment
 define BLURB
@@ -30,9 +30,9 @@
 CITE = doi:10.1038/nmeth.1923
 
 ######################################################################
-
-MASTER_SITES = $(MASTER_SOURCEFORGE)
-MASTER_SUBDIR = $(GARNAME)-bio/files/$(UPSTREAMNAME)/$(GARVERSION)/
+# https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1
+MASTER_SITES = $(MASTER_SOURCEFORGE)/
+MASTER_SUBDIR = bowtie-bio/files/$(GARNAME)/$(GARVERSION)/
 DISTFILES = $(DISTNAME)-source.zip
 BUILD_SCRIPTS = $(WORKSRC)/Makefile
 INSTALL_SCRIPTS = programs

=== modified file 'pkg/bio/bowtie2/sha256sums'
--- a/pkg/bio/bowtie/sha256sums 2016-06-17 19:57:40 +0000
+++ b/pkg/bio/bowtie2/sha256sums        2018-06-30 06:49:39 +0000
@@ -1,1 +1,1 @@
-1f3482bf31111dbfb8b547f984c4755296316f6c48c33c7d3cf19c814785d0aa  
download/bowtie2-2.2.4-source.zip
+a1efef603b91ecc11cfdb822087ae00ecf2dd922e03c85eea1ed7f8230c119dc  
download/bowtie2-2.3.4.1-source.zip