svn commit: r415914 - in head/biology: bcftools htslib samtools samtools/files
Kurt Jaeger
pi at FreeBSD.org
Thu May 26 20:28:57 UTC 2016
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 at 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 at 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 at 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 at 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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