diff options
| author | bacon <bacon@pkgsrc.org> | 2018-05-07 18:37:31 +0000 |
|---|---|---|
| committer | bacon <bacon@pkgsrc.org> | 2018-05-07 18:37:31 +0000 |
| commit | 5efad60e075673e1eed7ee6d42ac03c3d384fe4e (patch) | |
| tree | aea66fb10298c23d39a4b495079ad8e32fb80a08 /biology | |
| parent | ac7f2f2cb05096510c78cecbd43709e010c12ec0 (diff) | |
| download | pkgsrc-5efad60e075673e1eed7ee6d42ac03c3d384fe4e.tar.gz | |
biology/samtools: import samtools-1.8
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.
OK wiz@
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/samtools/DESCR | 3 | ||||
| -rw-r--r-- | biology/samtools/Makefile | 25 | ||||
| -rw-r--r-- | biology/samtools/PLIST | 24 | ||||
| -rw-r--r-- | biology/samtools/distinfo | 6 |
4 files changed, 58 insertions, 0 deletions
diff --git a/biology/samtools/DESCR b/biology/samtools/DESCR new file mode 100644 index 00000000000..23d11d1c81f --- /dev/null +++ b/biology/samtools/DESCR @@ -0,0 +1,3 @@ +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. diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile new file mode 100644 index 00000000000..3ea284938cf --- /dev/null +++ b/biology/samtools/Makefile @@ -0,0 +1,25 @@ +# $NetBSD: Makefile,v 1.1 2018/05/07 18:37:31 bacon Exp $ + +DISTNAME= samtools-1.8 +CATEGORIES= biology +MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/} +GITHUB_TAG= ${PKGVERSION_NOREV} + +MAINTAINER= bacon@NetBSD.org +HOMEPAGE= http://www.htslib.org/ +COMMENT= Tools for manipulating next-generation sequencing data +LICENSE= mit + +USE_TOOLS+= autoconf automake autoreconf gmake perl:run +GNU_CONFIGURE= yes +REPLACE_PERL= misc/*.pl misc/plot-bamstats test/test.pl +REPLACE_PYTHON= misc/*.py + +pre-configure: + cd ${WRKSRC} && autoreconf + +.include "../../mk/curses.buildlink3.mk" +.include "../../lang/python/application.mk" +.include "../../biology/htslib/buildlink3.mk" +.include "../../devel/zlib/buildlink3.mk" +.include "../../mk/bsd.pkg.mk" diff --git a/biology/samtools/PLIST b/biology/samtools/PLIST new file mode 100644 index 00000000000..7b812362b52 --- /dev/null +++ b/biology/samtools/PLIST @@ -0,0 +1,24 @@ +@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 diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo new file mode 100644 index 00000000000..59523c11fb1 --- /dev/null +++ b/biology/samtools/distinfo @@ -0,0 +1,6 @@ +$NetBSD: distinfo,v 1.1 2018/05/07 18:37:31 bacon Exp $ + +SHA1 (samtools-1.8.tar.gz) = 5ac70ba4c324c223398ab4c0689933564985303c +RMD160 (samtools-1.8.tar.gz) = 47e4fde82a686669322fd330374aa37b148b7954 +SHA512 (samtools-1.8.tar.gz) = 82e4d5f855f944cc989902154a99eada2b4c81939bd936fa1d471cf9ff01e03c8a7f773928ae55ef691f2827aa4076126678940bb89a322fa56d83c517677d0c +Size (samtools-1.8.tar.gz) = 4047378 bytes |