Date: Thu, 26 May 2016 20:28:55 +0000 (UTC) From: Kurt Jaeger <pi@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r415914 - in head/biology: bcftools htslib samtools samtools/files Message-ID: <201605262028.u4QKSudg006776@repo.freebsd.org>
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Author: pi Date: Thu May 26 20:28:55 2016 New Revision: 415914 URL: https://svnweb.freebsd.org/changeset/ports/415914 Log: biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1 Changes: https://sourceforge.net/p/samtools/mailman/message/35033807/ PR: 209653 Submitted by: cartwright@asu.edu (maintainer) Modified: head/biology/bcftools/Makefile head/biology/bcftools/distinfo head/biology/bcftools/pkg-plist head/biology/htslib/Makefile head/biology/htslib/distinfo head/biology/samtools/Makefile head/biology/samtools/distinfo head/biology/samtools/files/patch-Makefile Modified: head/biology/bcftools/Makefile ============================================================================== --- head/biology/bcftools/Makefile Thu May 26 20:01:01 2016 (r415913) +++ head/biology/bcftools/Makefile Thu May 26 20:28:55 2016 (r415914) @@ -2,19 +2,21 @@ # $FreeBSD$ 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 Modified: head/biology/bcftools/distinfo ============================================================================== --- head/biology/bcftools/distinfo Thu May 26 20:01:01 2016 (r415913) +++ head/biology/bcftools/distinfo Thu May 26 20:28:55 2016 (r415914) @@ -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 Modified: head/biology/bcftools/pkg-plist ============================================================================== --- head/biology/bcftools/pkg-plist Thu May 26 20:01:01 2016 (r415913) +++ head/biology/bcftools/pkg-plist Thu May 26 20:28:55 2016 (r415914) @@ -2,6 +2,7 @@ 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 Modified: head/biology/htslib/Makefile ============================================================================== --- head/biology/htslib/Makefile Thu May 26 20:01:01 2016 (r415913) +++ head/biology/htslib/Makefile Thu May 26 20:28:55 2016 (r415914) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= htslib -PORTVERSION= 1.3 +PORTVERSION= 1.3.1 CATEGORIES= biology devel MAINTAINER= cartwright@asu.edu @@ -21,7 +21,7 @@ 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 Modified: head/biology/htslib/distinfo ============================================================================== --- head/biology/htslib/distinfo Thu May 26 20:01:01 2016 (r415913) +++ head/biology/htslib/distinfo Thu May 26 20:28:55 2016 (r415914) @@ -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 Modified: head/biology/samtools/Makefile ============================================================================== --- head/biology/samtools/Makefile Thu May 26 20:01:01 2016 (r415913) +++ head/biology/samtools/Makefile Thu May 26 20:28:55 2016 (r415914) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= samtools -PORTVERSION= 1.3 +PORTVERSION= 1.3.1 CATEGORIES= biology MAINTAINER= cartwright@asu.edu Modified: head/biology/samtools/distinfo ============================================================================== --- head/biology/samtools/distinfo Thu May 26 20:01:01 2016 (r415913) +++ head/biology/samtools/distinfo Thu May 26 20:28:55 2016 (r415914) @@ -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 Modified: head/biology/samtools/files/patch-Makefile ============================================================================== --- head/biology/samtools/files/patch-Makefile Thu May 26 20:01:01 2016 (r415913) +++ head/biology/samtools/files/patch-Makefile Thu May 26 20:28:55 2016 (r415914) @@ -1,6 +1,6 @@ ---- 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 @@ -26,7 +26,7 @@ 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 = \ @@ -34,19 +34,16 @@ 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)
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