Index: head/biology/bcftools/Makefile =================================================================== --- head/biology/bcftools/Makefile (revision 415913) +++ head/biology/bcftools/Makefile (revision 415914) @@ -1,52 +1,54 @@ # Created by: Reed A. Cartwright # $FreeBSD$ PORTNAME= bcftools -PORTVERSION= 1.3 +PORTVERSION= 1.3.1 CATEGORIES= biology MAINTAINER= cartwright@asu.edu COMMENT= Tools for manipulating next-generation sequencing data LICENSE= MIT -LICENSE_FILE= ${WRKSRC}/LICENSE +# LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= htslib>=1.3:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib TEST_DEPENDS= bash:shells/bash + +CONFLICTS_BUILD=openssl USE_GITHUB= yes GH_ACCOUNT= samtools USES= gmake perl5 shebangfix USE_PERL5= test SUB_FILES= pkg-message SHEBANG_FILES= vcfutils.pl plot-vcfstats plugins/color-chrs.pl test/test.pl OPTIONS_DEFINE= GPL GPL_DESC= Enable modules that rely on GPL code OPTIONS_DEFAULT= GPL GPL_LIB_DEPENDS= libgsl.so:math/gsl .include CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \ INSTALL_DATA="${INSTALL_DATA}" \ INSTALL_PROGRAM="${INSTALL_PROGRAM}" \ INSTALL_SCRIPT="${INSTALL_SCRIPT}" \ INSTALL_DIR="${MKDIR}" .if ${PORT_OPTIONS:MGPL} MAKE_ENV+= USE_GPL=1 LICENSE= GPLv3 .endif PLIST_SUB= PORTVERSION="${PORTVERSION}" TEST_TARGET= test .include Index: head/biology/bcftools/distinfo =================================================================== --- head/biology/bcftools/distinfo (revision 415913) +++ head/biology/bcftools/distinfo (revision 415914) @@ -1,2 +1,3 @@ -SHA256 (samtools-bcftools-1.3_GH0.tar.gz) = 3f4d4bf68637070cb7dbb5d5619ece7e3315727e651eab751d849085439b11d8 -SIZE (samtools-bcftools-1.3_GH0.tar.gz) = 943041 +TIMESTAMP = 1463692643 +SHA256 (samtools-bcftools-1.3.1_GH0.tar.gz) = 99a5cc05faa974f5ddbeebf346bb51a806bdaaf8e2f6adc3bead28551983e77e +SIZE (samtools-bcftools-1.3.1_GH0.tar.gz) = 958207 Index: head/biology/bcftools/pkg-plist =================================================================== --- head/biology/bcftools/pkg-plist (revision 415913) +++ head/biology/bcftools/pkg-plist (revision 415914) @@ -1,18 +1,19 @@ bin/bcftools bin/samtools_misc/color-chrs.pl bin/samtools_misc/plot-vcfstats bin/samtools_misc/vcfutils.pl +libexec/bcftools/GTisec.so libexec/bcftools/color-chrs.so libexec/bcftools/counts.so libexec/bcftools/dosage.so libexec/bcftools/fill-AN-AC.so libexec/bcftools/fill-tags.so libexec/bcftools/fixploidy.so libexec/bcftools/frameshifts.so libexec/bcftools/impute-info.so libexec/bcftools/mendelian.so libexec/bcftools/missing2ref.so libexec/bcftools/setGT.so libexec/bcftools/tag2tag.so libexec/bcftools/vcf2sex.so man/man1/bcftools.1.gz Index: head/biology/htslib/Makefile =================================================================== --- head/biology/htslib/Makefile (revision 415913) +++ head/biology/htslib/Makefile (revision 415914) @@ -1,48 +1,48 @@ # Created by: Reed A. Cartwright # $FreeBSD$ PORTNAME= htslib -PORTVERSION= 1.3 +PORTVERSION= 1.3.1 CATEGORIES= biology devel MAINTAINER= cartwright@asu.edu COMMENT= C library for high-throughput sequencing data formats LICENSE= BSD3CLAUSE MIT LICENSE_COMB= multi LICENSE_FILE= ${WRKSRC}/LICENSE TEST_DEPENDS= bash:shells/bash USE_GITHUB= yes GH_ACCOUNT= samtools USES= autoreconf gmake perl5 shebangfix USE_PERL5= test USE_LDCONFIG= yes GNU_CONFIGURE= yes -SHEBANG_FILES= test/compare_sam.pl test/test.pl test/test_view.pl +SHEBANG_FILES= test/compare_sam.pl test/test.pl OPTIONS_DEFINE= CURL OPTIONS_DEFAULT= CURL CURL_DESC= Use libcurl for network file access (HTTPS and S3 support). CURL_LIB_DEPENDS= libcurl.so:ftp/curl CURL_CONFIGURE_ENABLE= libcurl CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \ INSTALL_DATA="${INSTALL_DATA}" \ INSTALL_PROGRAM="${INSTALL_PROGRAM}" \ INSTALL_DIR="${MKDIR}" PLIST_SUB= PORTVERSION="${PORTVERSION}" TEST_TARGET= test post-patch: @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac .include Index: head/biology/htslib/distinfo =================================================================== --- head/biology/htslib/distinfo (revision 415913) +++ head/biology/htslib/distinfo (revision 415914) @@ -1,2 +1,3 @@ -SHA256 (samtools-htslib-1.3_GH0.tar.gz) = 291a54090df3bc367b509890e1cfa34d53b1ee9be42c5fa6c2b1e2ec8f8b13af -SIZE (samtools-htslib-1.3_GH0.tar.gz) = 1042953 +TIMESTAMP = 1463688817 +SHA256 (samtools-htslib-1.3.1_GH0.tar.gz) = 3bbd04f9a0c4c301abd5d19a81920894ac2ee5e86e8aa977e8c2035e01d93ea7 +SIZE (samtools-htslib-1.3.1_GH0.tar.gz) = 1065840 Index: head/biology/samtools/Makefile =================================================================== --- head/biology/samtools/Makefile (revision 415913) +++ head/biology/samtools/Makefile (revision 415914) @@ -1,44 +1,44 @@ # Created by: Reed A. Cartwright # $FreeBSD$ PORTNAME= samtools -PORTVERSION= 1.3 +PORTVERSION= 1.3.1 CATEGORIES= biology MAINTAINER= cartwright@asu.edu COMMENT= Tools for manipulating next-generation sequencing data LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= htslib>=1.3:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib TEST_DEPENDS= bash:shells/bash USE_GITHUB= yes USES= autoreconf gmake ncurses perl5 shebangfix USE_PERL5= test GNU_CONFIGURE= yes SUB_FILES= pkg-message SHEBANG_FILES= misc/*.pl misc/plot-bamstats test/test.pl CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \ INSTALL_DATA="${INSTALL_DATA}" \ INSTALL_PROGRAM="${INSTALL_PROGRAM}" \ INSTALL_SCRIPT="${INSTALL_SCRIPT}" \ INSTALL_DIR="${MKDIR}" PLIST_SUB= PORTVERSION="${PORTVERSION}" TEST_TARGET= test post-patch: @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac ${CP} ${FILESDIR}/ax_with_htslib.m4 ${WRKSRC}/ ${CP} ${FILESDIR}/ax_with_curses.m4 ${WRKSRC}/ .include Index: head/biology/samtools/distinfo =================================================================== --- head/biology/samtools/distinfo (revision 415913) +++ head/biology/samtools/distinfo (revision 415914) @@ -1,2 +1,3 @@ -SHA256 (samtools-samtools-1.3_GH0.tar.gz) = f1eee9a217d547d9b483098519738ef351ec454f4a85cdb1e77ae8892fe858b5 -SIZE (samtools-samtools-1.3_GH0.tar.gz) = 3742904 +TIMESTAMP = 1463691050 +SHA256 (samtools-samtools-1.3.1_GH0.tar.gz) = 30752c7b92cd9e146f4017983b2a41beb58c8966e93572cea76a14719f95a768 +SIZE (samtools-samtools-1.3.1_GH0.tar.gz) = 3757176 Index: head/biology/samtools/files/patch-Makefile =================================================================== --- head/biology/samtools/files/patch-Makefile (revision 415913) +++ head/biology/samtools/files/patch-Makefile (revision 415914) @@ -1,61 +1,58 @@ ---- Makefile.orig 2015-12-15 21:26:20 UTC +--- Makefile.orig 2016-04-22 09:22:44 UTC +++ Makefile -@@ -39,18 +39,18 @@ AOBJS= bam_index.o bam_plcmd.o sam_ +@@ -38,18 +38,18 @@ AOBJS= bam_index.o bam_plcmd.o sam_ bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ bam_quickcheck.o bam_addrprg.o -prefix = /usr/local +prefix = ${STAGEDIR}${PREFIX} exec_prefix = $(prefix) bindir = $(exec_prefix)/bin datarootdir = $(prefix)/share -mandir = $(datarootdir)/man +mandir = $(prefix)/man man1dir = $(mandir)/man1 -MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_PROGRAM = $(INSTALL) -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 +#MKDIR_P = mkdir -p +#INSTALL = install -p +#INSTALL_PROGRAM = $(INSTALL) +#INSTALL_DATA = $(INSTALL) -m 644 +#INSTALL_DIR = $(MKDIR_P) -m 755 PROGRAMS = samtools -@@ -60,7 +60,6 @@ BUILT_MISC_PROGRAMS = \ +@@ -59,7 +59,6 @@ BUILT_MISC_PROGRAMS = \ misc/md5fa misc/md5sum-lite misc/wgsim MISC_PROGRAMS = \ - $(BUILT_MISC_PROGRAMS) \ misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \ misc/interpolate_sam.pl misc/novo2sam.pl \ misc/plot-bamstats misc/psl2sam.pl \ -@@ -81,9 +80,9 @@ BUILT_TEST_PROGRAMS = \ - all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) - +@@ -82,7 +81,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally --ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) -+ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) + ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) -ALL_LIBS = -lz -ldl $(LIBS) +ALL_LIBS = -lz $(LIBS) # Usually config.mk and config.h are generated by running configure # or config.status, but if those aren't used create defaults here. -@@ -280,8 +279,10 @@ misc/maq2sam-long.o: misc/maq2sam.c +@@ -280,8 +279,10 @@ misc/maq2sam-long.o: misc/maq2sam.c conf install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) - $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir) + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) + $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) + $(INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc + $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc $(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir)