Index: head/biology/htslib/Makefile =================================================================== --- head/biology/htslib/Makefile (revision 474751) +++ head/biology/htslib/Makefile (revision 474752) @@ -1,41 +1,38 @@ # Created by: Reed A. Cartwright # $FreeBSD$ PORTNAME= htslib -PORTVERSION= 1.6 +DISTVERSION= 1.8 CATEGORIES= biology devel MAINTAINER= cartwright@asu.edu COMMENT= C library for high-throughput sequencing data formats LICENSE= BSD3CLAUSE MIT LICENSE_COMB= multi LICENSE_FILE= ${WRKSRC}/LICENSE TEST_DEPENDS= bash:shells/bash +USES= autoreconf gmake localbase pathfix perl5 shebangfix USE_GITHUB= yes GH_ACCOUNT= samtools - -USES= autoreconf gmake pathfix perl5 shebangfix USE_PERL5= test USE_LDCONFIG= yes GNU_CONFIGURE= yes PATHFIX_MAKEFILEIN= Makefile SHEBANG_FILES= test/compare_sam.pl test/test.pl OPTIONS_DEFINE= CURL OPTIONS_DEFAULT= CURL CURL_DESC= Use libcurl for network file access (HTTPS and S3 support). +CURL_USES= ssl CURL_LIB_DEPENDS= libcurl.so:ftp/curl CURL_CONFIGURE_ENABLE= libcurl - -CPPFLAGS+= -I${LOCALBASE}/include -LDFLAGS+= -L${LOCALBASE}/lib PLIST_SUB= PORTVERSION="${PORTVERSION}" TEST_TARGET= test .include Index: head/biology/htslib/distinfo =================================================================== --- head/biology/htslib/distinfo (revision 474751) +++ head/biology/htslib/distinfo (revision 474752) @@ -1,3 +1,3 @@ -TIMESTAMP = 1508301522 -SHA256 (samtools-htslib-1.6_GH0.tar.gz) = 4215c9153c27603cbaaf542f2ec128c5e839380d6df6edd4dbf67955170740c6 -SIZE (samtools-htslib-1.6_GH0.tar.gz) = 1155672 +TIMESTAMP = 1528766078 +SHA256 (samtools-htslib-1.8_GH0.tar.gz) = ad52105c0f9ce6474c8f5d2f208b8e71982436ee1ca5225162932b08aff48b23 +SIZE (samtools-htslib-1.8_GH0.tar.gz) = 1262465 Index: head/biology/htslib/pkg-descr =================================================================== --- head/biology/htslib/pkg-descr (revision 474751) +++ head/biology/htslib/pkg-descr (revision 474752) @@ -1,5 +1,5 @@ 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. -WWW: http://www.htslib.org/ +WWW: https://www.htslib.org/ Index: head/biology/htslib/pkg-plist =================================================================== --- head/biology/htslib/pkg-plist (revision 474751) +++ head/biology/htslib/pkg-plist (revision 474752) @@ -1,39 +1,40 @@ 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.%%PORTVERSION%% lib/libhts.so.2 libdata/pkgconfig/htslib.pc +man/man1/bgzip.1.gz man/man1/htsfile.1.gz man/man1/tabix.1.gz man/man5/faidx.5.gz man/man5/sam.5.gz man/man5/vcf.5.gz