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Bacon" Date: Sat, 12 Jan 2019 15:53:01 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r490062 - in head/biology/stacks: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology/stacks: . files X-SVN-Commit-Revision: 490062 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: BE0698B984 X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.93 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.999,0]; NEURAL_HAM_LONG(-1.00)[-0.999,0]; NEURAL_HAM_SHORT(-0.93)[-0.931,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US] X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 12 Jan 2019 15:53:02 -0000 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@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 .if ${ARCH} != amd64 && ${ARCH} != i386 -USE_GCC= yes +USE_GCC= yes .endif .include 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