CVS commit: pkgsrc/biology

["Adam Ciarcinski" <adam%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   adam
Date:           Thu Nov 15 09:21:24 UTC 2018

Modified Files:
        pkgsrc/biology: Makefile
Added Files:
        pkgsrc/biology/bcftools: DESCR Makefile PLIST distinfo

Log Message:
bcftools: added version 1.9

BCFtools is a program for variant calling and manipulating files in the Variant
Call Format (VCF) and its binary counterpart BCF. All commands work
transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
In order to avoid tedious repetion, throughout this document we will use "VCF"
and "BCF" interchangeably, unless specifically noted.

Most commands accept VCF, bgzipped VCF and BCF with filetype detected
automatically even when streaming from a pipe. Indexed VCF and BCF work in all
situations. Unindexed VCF and BCF and streams work in most, but not all
situations. In general, whenever multiple VCFs are read simultaneously, they
must be indexed and therefore also compressed.


To generate a diff of this commit:
cvs rdiff -u -r1.47 -r1.48 pkgsrc/biology/Makefile
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/bcftools/DESCR \
    pkgsrc/biology/bcftools/Makefile pkgsrc/biology/bcftools/PLIST \
    pkgsrc/biology/bcftools/distinfo

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

Modified files:

Index: pkgsrc/biology/Makefile
diff -u pkgsrc/biology/Makefile:1.47 pkgsrc/biology/Makefile:1.48
--- pkgsrc/biology/Makefile:1.47        Wed Oct 31 20:16:30 2018
+++ pkgsrc/biology/Makefile     Thu Nov 15 09:21:24 2018
@@ -1,10 +1,11 @@
-# $NetBSD: Makefile,v 1.47 2018/10/31 20:16:30 leot Exp $
+# $NetBSD: Makefile,v 1.48 2018/11/15 09:21:24 adam Exp $
 #
 
 COMMENT=       Software for the biological sciences
 
 SUBDIR+=       arka
 SUBDIR+=       azara
+SUBDIR+=       bcftools
 SUBDIR+=       bioperl
 SUBDIR+=       bodr
 SUBDIR+=       bwa

Added files:

Index: pkgsrc/biology/bcftools/DESCR
diff -u /dev/null pkgsrc/biology/bcftools/DESCR:1.1
--- /dev/null   Thu Nov 15 09:21:24 2018
+++ pkgsrc/biology/bcftools/DESCR       Thu Nov 15 09:21:24 2018
@@ -0,0 +1,11 @@
+BCFtools is a program for variant calling and manipulating files in the Variant
+Call Format (VCF) and its binary counterpart BCF. All commands work
+transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
+In order to avoid tedious repetion, throughout this document we will use "VCF"
+and "BCF" interchangeably, unless specifically noted.
+
+Most commands accept VCF, bgzipped VCF and BCF with filetype detected
+automatically even when streaming from a pipe. Indexed VCF and BCF work in all
+situations. Unindexed VCF and BCF and streams work in most, but not all
+situations. In general, whenever multiple VCFs are read simultaneously, they
+must be indexed and therefore also compressed.
Index: pkgsrc/biology/bcftools/Makefile
diff -u /dev/null pkgsrc/biology/bcftools/Makefile:1.1
--- /dev/null   Thu Nov 15 09:21:24 2018
+++ pkgsrc/biology/bcftools/Makefile    Thu Nov 15 09:21:24 2018
@@ -0,0 +1,28 @@
+# $NetBSD: Makefile,v 1.1 2018/11/15 09:21:24 adam Exp $
+
+DISTNAME=      bcftools-1.9
+CATEGORIES=    biology
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
+EXTRACT_SUFX=  .tar.bz2
+GITHUB_RELEASE=        ${PKGVERSION_NOREV}
+
+MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=      http://samtools.github.io/bcftools/
+COMMENT=       Calling and manipulating files VCF and BCF formats
+LICENSE=       mit
+
+USE_TOOLS+=            gmake perl
+GNU_CONFIGURE=         yes
+CONFIGURE_ARGS+=       --with-htslib=system
+TEST_TARGET=           test
+
+BUILDLINK_TRANSFORM+=   opt:-ldl:${BUILDLINK_LDADD.dl:M*}
+
+REPLACE_PERL+=         misc/*.pl
+REPLACE_PERL+=         misc/plot-vcfstats
+REPLACE_PYTHON+=       misc/*.py
+
+.include "../../biology/htslib/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/dlopen.buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/bcftools/PLIST
diff -u /dev/null pkgsrc/biology/bcftools/PLIST:1.1
--- /dev/null   Thu Nov 15 09:21:24 2018
+++ pkgsrc/biology/bcftools/PLIST       Thu Nov 15 09:21:24 2018
@@ -0,0 +1,37 @@
+@comment $NetBSD: PLIST,v 1.1 2018/11/15 09:21:24 adam Exp $
+bin/bcftools
+bin/color-chrs.pl
+bin/guess-ploidy.py
+bin/plot-roh.py
+bin/plot-vcfstats
+bin/run-roh.pl
+bin/vcfutils.pl
+libexec/bcftools/GTisec.so
+libexec/bcftools/GTsubset.so
+libexec/bcftools/ad-bias.so
+libexec/bcftools/af-dist.so
+libexec/bcftools/check-ploidy.so
+libexec/bcftools/check-sparsity.so
+libexec/bcftools/color-chrs.so
+libexec/bcftools/contrast.so
+libexec/bcftools/counts.so
+libexec/bcftools/dosage.so
+libexec/bcftools/fill-AN-AC.so
+libexec/bcftools/fill-from-fasta.so
+libexec/bcftools/fill-tags.so
+libexec/bcftools/fixploidy.so
+libexec/bcftools/fixref.so
+libexec/bcftools/frameshifts.so
+libexec/bcftools/guess-ploidy.so
+libexec/bcftools/impute-info.so
+libexec/bcftools/isecGT.so
+libexec/bcftools/mendelian.so
+libexec/bcftools/missing2ref.so
+libexec/bcftools/prune.so
+libexec/bcftools/setGT.so
+libexec/bcftools/smpl-stats.so
+libexec/bcftools/split.so
+libexec/bcftools/tag2tag.so
+libexec/bcftools/trio-stats.so
+libexec/bcftools/trio-switch-rate.so
+man/man1/bcftools.1
Index: pkgsrc/biology/bcftools/distinfo
diff -u /dev/null pkgsrc/biology/bcftools/distinfo:1.1
--- /dev/null   Thu Nov 15 09:21:24 2018
+++ pkgsrc/biology/bcftools/distinfo    Thu Nov 15 09:21:24 2018
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2018/11/15 09:21:24 adam Exp $
+
+SHA1 (bcftools-1.9.tar.bz2) = 9b649c3f407528ee193210f68b8e21e8b0aebf31
+RMD160 (bcftools-1.9.tar.bz2) = 59b9997aaa509ba84c41b7e78821f31eca8d90dc
+SHA512 (bcftools-1.9.tar.bz2) = fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c
+Size (bcftools-1.9.tar.bz2) = 3134355 bytes