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samtools: Remove, same version already in biology

This commit is contained in:
Jason Bacon 2019-05-04 11:22:50 -05:00
parent 6c33f11240
commit 2ab60451a2
7 changed files with 1 additions and 66 deletions
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1
Makefile
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@ -4346,7 +4346,6 @@ SUBDIR+= sais
SUBDIR+= sais-demo-data
SUBDIR+= salmon
SUBDIR+= samhain
SUBDIR+= samtools
SUBDIR+= samtools0119
SUBDIR+= sara
SUBDIR+= sarf

2
ddocent/Makefile
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@ -27,7 +27,7 @@ DEPENDS= mawk>=0:../../lang/mawk \
parallel>=0:../../parallel/parallel \
bwa>=0.7.13:../../biology/bwa \
cdhit>=0:../../biology/cdhit \
samtools>=1.3:../../wip/samtools \
samtools>=1.3:../../biology/samtools \
vcftools>=0.1.15:../../wip/vcftools \
Trimmomatic>=0:../../biology/trimmomatic \
stacks>=0:../../biology/stacks \

3
samtools/DESCR
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@ -1,3 +0,0 @@
Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.

28
samtools/Makefile
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@ -1,28 +0,0 @@
# $NetBSD: Makefile,v 1.3 2018/11/06 10:49:41 adam Exp $
DISTNAME= samtools-1.9
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/}
EXTRACT_SUFX= .tar.bz2
GITHUB_RELEASE= ${PKGVERSION_NOREV}
MAINTAINER= bacon@NetBSD.org
HOMEPAGE= http://www.htslib.org/
COMMENT= Tools for manipulating next-generation sequencing data
LICENSE= mit
USE_TOOLS+= gmake perl:run
GNU_CONFIGURE= yes
CONFIGURE_ARGS+= --with-htslib=system
TEST_TARGET= test
REPLACE_PERL= misc/*.pl
REPLACE_PERL+= misc/plot-bamstats
REPLACE_PERL+= test/test.pl
REPLACE_PYTHON= misc/*.py
.include "../../devel/zlib/buildlink3.mk"
.include "../../wip/htslib/buildlink3.mk"
.include "../../lang/python/application.mk"
.include "../../mk/curses.buildlink3.mk"
.include "../../mk/bsd.pkg.mk"

24
samtools/PLIST
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@ -1,24 +0,0 @@
@comment $NetBSD: PLIST,v 1.1 2018/05/07 18:37:31 bacon Exp $
bin/ace2sam
bin/blast2sam.pl
bin/bowtie2sam.pl
bin/export2sam.pl
bin/interpolate_sam.pl
bin/maq2sam-long
bin/maq2sam-short
bin/md5fa
bin/md5sum-lite
bin/novo2sam.pl
bin/plot-bamstats
bin/psl2sam.pl
bin/sam2vcf.pl
bin/samtools
bin/samtools.pl
bin/seq_cache_populate.pl
bin/soap2sam.pl
bin/varfilter.py
bin/wgsim
bin/wgsim_eval.pl
bin/zoom2sam.pl
man/man1/samtools.1
man/man1/wgsim.1

3
samtools/TODO
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@ -1,3 +0,0 @@
Figure out who removed zlib/bl3 in biology/samtools
Address vulnerability

6
samtools/distinfo
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@ -1,6 +0,0 @@
$NetBSD: distinfo,v 1.2 2018/11/06 10:49:41 adam Exp $
SHA1 (samtools-1.9.tar.bz2) = 267191dc2f5d24eb0b22c0094138270ed5384241
RMD160 (samtools-1.9.tar.bz2) = b7f49e1bdd569f63ec53330f43df7e5566ba8a16
SHA512 (samtools-1.9.tar.bz2) = 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f
Size (samtools-1.9.tar.bz2) = 4440405 bytes