CVS commit: pkgsrc/biology/samtools

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Mon May  7 18:37:31 UTC 2018

Added Files:
        pkgsrc/biology/samtools: DESCR Makefile PLIST distinfo

Log Message:
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@


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/samtools/DESCR \
    pkgsrc/biology/samtools/Makefile pkgsrc/biology/samtools/PLIST \
    pkgsrc/biology/samtools/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Added files:

Index: pkgsrc/biology/samtools/DESCR
diff -u /dev/null pkgsrc/biology/samtools/DESCR:1.1
--- /dev/null   Mon May  7 18:37:31 2018
+++ pkgsrc/biology/samtools/DESCR       Mon May  7 18:37:31 2018
@@ -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.
Index: pkgsrc/biology/samtools/Makefile
diff -u /dev/null pkgsrc/biology/samtools/Makefile:1.1
--- /dev/null   Mon May  7 18:37:31 2018
+++ pkgsrc/biology/samtools/Makefile    Mon May  7 18:37:31 2018
@@ -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@localhost
+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"
Index: pkgsrc/biology/samtools/PLIST
diff -u /dev/null pkgsrc/biology/samtools/PLIST:1.1
--- /dev/null   Mon May  7 18:37:31 2018
+++ pkgsrc/biology/samtools/PLIST       Mon May  7 18:37:31 2018
@@ -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
Index: pkgsrc/biology/samtools/distinfo
diff -u /dev/null pkgsrc/biology/samtools/distinfo:1.1
--- /dev/null   Mon May  7 18:37:31 2018
+++ pkgsrc/biology/samtools/distinfo    Mon May  7 18:37:31 2018
@@ -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