CVS commit: pkgsrc/biology/htslib

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Mon Apr 30 16:51:54 UTC 2018

Added Files:
        pkgsrc/biology/htslib: DESCR Makefile PLIST buildlink3.mk distinfo

Log Message:
biology/htslib: import htslib-1.8

HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/htslib/DESCR \
    pkgsrc/biology/htslib/Makefile pkgsrc/biology/htslib/PLIST \
    pkgsrc/biology/htslib/buildlink3.mk pkgsrc/biology/htslib/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/htslib/DESCR
diff -u /dev/null pkgsrc/biology/htslib/DESCR:1.1
--- /dev/null   Mon Apr 30 16:51:54 2018
+++ pkgsrc/biology/htslib/DESCR Mon Apr 30 16:51:54 2018
@@ -0,0 +1,3 @@
+HTSlib is an implementation of a unified C library for accessing common file
+formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
+data. It is the core library used by samtools and bcftools.
Index: pkgsrc/biology/htslib/Makefile
diff -u /dev/null pkgsrc/biology/htslib/Makefile:1.1
--- /dev/null   Mon Apr 30 16:51:54 2018
+++ pkgsrc/biology/htslib/Makefile      Mon Apr 30 16:51:54 2018
@@ -0,0 +1,31 @@
+# $NetBSD: Makefile,v 1.1 2018/04/30 16:51:54 bacon Exp $
+
+DISTNAME=      htslib-1.8
+CATEGORIES=    biology
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
+GITHUB_PROJECT=        htslib
+GITHUB_TAG=    ${PKGVERSION_NOREV}
+
+MAINTAINER=    bacon%NetBSD.org@localhost
+HOMEPAGE=      http://www.htslib.org/
+COMMENT=       C library for high-throughput sequencing data formats
+LICENSE=       mit
+
+USE_TOOLS+=    autoconf automake autoreconf gmake perl
+GNU_CONFIGURE= yes
+REPLACE_PERL=  test/compare_sam.pl test/test.pl
+
+SUBST_CLASSES+=                version
+SUBST_STAGE.version=   post-patch
+SUBST_SED.version=     -e "s|m4_esyscmd_s(\[make print-version\])|[${PKGVERSION_NOREV}]|"
+SUBST_FILES.version=   ${WRKSRC}/configure.ac
+
+PKGCONFIG_OVERRIDE=    htslib.pc.in
+
+pre-configure:
+       cd ${WRKSRC} && autoreconf
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../archivers/xz/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/htslib/PLIST
diff -u /dev/null pkgsrc/biology/htslib/PLIST:1.1
--- /dev/null   Mon Apr 30 16:51:54 2018
+++ pkgsrc/biology/htslib/PLIST Mon Apr 30 16:51:54 2018
@@ -0,0 +1,41 @@
+@comment $NetBSD: PLIST,v 1.1 2018/04/30 16:51:54 bacon Exp $
+bin/bgzip
+bin/htsfile
+bin/tabix
+include/htslib/bgzf.h
+include/htslib/cram.h
+include/htslib/faidx.h
+include/htslib/hfile.h
+include/htslib/hts.h
+include/htslib/hts_defs.h
+include/htslib/hts_endian.h
+include/htslib/hts_log.h
+include/htslib/hts_os.h
+include/htslib/kbitset.h
+include/htslib/kfunc.h
+include/htslib/khash.h
+include/htslib/khash_str2int.h
+include/htslib/klist.h
+include/htslib/knetfile.h
+include/htslib/kseq.h
+include/htslib/ksort.h
+include/htslib/kstring.h
+include/htslib/regidx.h
+include/htslib/sam.h
+include/htslib/synced_bcf_reader.h
+include/htslib/tbx.h
+include/htslib/thread_pool.h
+include/htslib/vcf.h
+include/htslib/vcf_sweep.h
+include/htslib/vcfutils.h
+lib/libhts.a
+lib/libhts.so
+lib/libhts.so.${PKGVERSION}
+lib/libhts.so.2
+lib/pkgconfig/htslib.pc
+man/man1/bgzip.1
+man/man1/htsfile.1
+man/man1/tabix.1
+man/man5/faidx.5
+man/man5/sam.5
+man/man5/vcf.5
Index: pkgsrc/biology/htslib/buildlink3.mk
diff -u /dev/null pkgsrc/biology/htslib/buildlink3.mk:1.1
--- /dev/null   Mon Apr 30 16:51:54 2018
+++ pkgsrc/biology/htslib/buildlink3.mk Mon Apr 30 16:51:54 2018
@@ -0,0 +1,13 @@
+# $NetBSD: buildlink3.mk,v 1.1 2018/04/30 16:51:54 bacon Exp $
+
+BUILDLINK_TREE+=       htslib
+
+.if !defined(HTSLIB_BUILDLINK3_MK)
+HTSLIB_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.htslib+= htslib>=1.8
+BUILDLINK_PKGSRCDIR.htslib?=   ../../wip/htslib
+
+.endif # HTSLIB_BUILDLINK3_MK
+
+BUILDLINK_TREE+=       -htslib
Index: pkgsrc/biology/htslib/distinfo
diff -u /dev/null pkgsrc/biology/htslib/distinfo:1.1
--- /dev/null   Mon Apr 30 16:51:54 2018
+++ pkgsrc/biology/htslib/distinfo      Mon Apr 30 16:51:54 2018
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2018/04/30 16:51:54 bacon Exp $
+
+SHA1 (htslib-1.8.tar.gz) = bc9dd2ca08de99b0b30bb7f5d64bfa0e8c3d35fd
+RMD160 (htslib-1.8.tar.gz) = 400ee0a4994c01e314394bd6a2dceedaa93ec7af
+SHA512 (htslib-1.8.tar.gz) = 888c815d5b202a624cfc99dfe4f795825defd4dcd2420153314096c8fe79532e0a21e0be6bd3b5a4f86dfa1e7c4524271b3f960ab871812abe5a1961d05d568c
+Size (htslib-1.8.tar.gz) = 1262465 bytes