svn commit: r490062 - in head/biology/stacks: . files
Jason W. Bacon
jwb at FreeBSD.org
Sat Jan 12 15:53:02 UTC 2019
Author: jwb
Date: Sat Jan 12 15:53:00 2019
New Revision: 490062
URL: https://svnweb.freebsd.org/changeset/ports/490062
Log:
biology/stacks: Upgrade to 2.3
Approved by: jrm (mentor, implicit)
Deleted:
head/biology/stacks/files/
Modified:
head/biology/stacks/Makefile
head/biology/stacks/distinfo
head/biology/stacks/pkg-plist
Modified: head/biology/stacks/Makefile
==============================================================================
--- head/biology/stacks/Makefile Sat Jan 12 15:39:59 2019 (r490061)
+++ head/biology/stacks/Makefile Sat Jan 12 15:53:00 2019 (r490062)
@@ -1,9 +1,8 @@
# $FreeBSD$
PORTNAME= stacks
-DISTVERSION= 1.48
-PORTREVISION= 3
-CATEGORIES= biology
+DISTVERSION= 2.3
+CATEGORIES= biology perl5 python
MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/
MAINTAINER= jwb at FreeBSD.org
@@ -13,7 +12,9 @@ LICENSE= GPLv2
LICENSE_FILE= ${WRKSRC}/LICENSE
USES= compiler:openmp gmake python shebangfix
-SHEBANG_FILES= scripts/*.pl scripts/*.py
+
+SHEBANG_FILES= scripts/*.pl scripts/*.py \
+ scripts/stacks-integrate-alignments scripts/stacks-gdb
GNU_CONFIGURE= yes
LDFLAGS+= -lpthread
@@ -21,7 +22,7 @@ LDFLAGS+= -lpthread
.include <bsd.port.pre.mk>
.if ${ARCH} != amd64 && ${ARCH} != i386
-USE_GCC= yes
+USE_GCC= yes
.endif
.include <bsd.port.post.mk>
Modified: head/biology/stacks/distinfo
==============================================================================
--- head/biology/stacks/distinfo Sat Jan 12 15:39:59 2019 (r490061)
+++ head/biology/stacks/distinfo Sat Jan 12 15:53:00 2019 (r490062)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1520376299
-SHA256 (stacks-1.48.tar.gz) = e9f6251f5f609f9dd0bb1de17a51f69ce1a9af531548c4d2456a89783b1dcd1e
-SIZE (stacks-1.48.tar.gz) = 895195
+TIMESTAMP = 1547306940
+SHA256 (stacks-2.3.tar.gz) = 2a5befaf11ca2f191afcd42a3a3392290d6a116d7fe737b69a2c4d5b77f40c99
+SIZE (stacks-2.3.tar.gz) = 10962586
Modified: head/biology/stacks/pkg-plist
==============================================================================
--- head/biology/stacks/pkg-plist Sat Jan 12 15:39:59 2019 (r490061)
+++ head/biology/stacks/pkg-plist Sat Jan 12 15:53:00 2019 (r490062)
@@ -2,24 +2,19 @@ bin/clone_filter
bin/count_fixed_catalog_snps.py
bin/cstacks
bin/denovo_map.pl
-bin/exec_velvet.pl
-bin/export_sql.pl
-bin/genotypes
-bin/index_radtags.pl
+bin/gstacks
bin/integrate_alignments.py
bin/kmer_filter
-bin/load_radtags.pl
-bin/load_sequences.pl
bin/phasedstacks
bin/populations
bin/process_radtags
bin/process_shortreads
-bin/pstacks
bin/ref_map.pl
-bin/rxstacks
-bin/sort_read_pairs.pl
bin/sstacks
-bin/stacks_export_notify.pl
+bin/stacks-dist-extract
+bin/stacks-gdb
+bin/stacks-integrate-alignments
+bin/tsv2bam
bin/ustacks
%%DATADIR%%/php/CatalogClass.php
%%DATADIR%%/php/Locus.php
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