diff options
author | bacon <bacon@pkgsrc.org> | 2018-04-30 16:51:54 +0000 |
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committer | bacon <bacon@pkgsrc.org> | 2018-04-30 16:51:54 +0000 |
commit | a39de021974009f8b0ce748544d10a406ab7cfd1 (patch) | |
tree | 8ca8b54339e01c9b408b98ec06c3d04789989421 /biology | |
parent | 3418d9ae09e24f3367ea8c4491b18fecb3e56593 (diff) | |
download | pkgsrc-a39de021974009f8b0ce748544d10a406ab7cfd1.tar.gz |
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.
Diffstat (limited to 'biology')
-rw-r--r-- | biology/htslib/DESCR | 3 | ||||
-rw-r--r-- | biology/htslib/Makefile | 31 | ||||
-rw-r--r-- | biology/htslib/PLIST | 41 | ||||
-rw-r--r-- | biology/htslib/buildlink3.mk | 13 | ||||
-rw-r--r-- | biology/htslib/distinfo | 6 |
5 files changed, 94 insertions, 0 deletions
diff --git a/biology/htslib/DESCR b/biology/htslib/DESCR new file mode 100644 index 00000000000..050ad06ba93 --- /dev/null +++ b/biology/htslib/DESCR @@ -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. diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile new file mode 100644 index 00000000000..19525f4b265 --- /dev/null +++ b/biology/htslib/Makefile @@ -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 +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" diff --git a/biology/htslib/PLIST b/biology/htslib/PLIST new file mode 100644 index 00000000000..ca2d06e3dda --- /dev/null +++ b/biology/htslib/PLIST @@ -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 diff --git a/biology/htslib/buildlink3.mk b/biology/htslib/buildlink3.mk new file mode 100644 index 00000000000..8862f6018d0 --- /dev/null +++ b/biology/htslib/buildlink3.mk @@ -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 diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo new file mode 100644 index 00000000000..43a9456bbdc --- /dev/null +++ b/biology/htslib/distinfo @@ -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 |