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biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1

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Changes:
  https://sourceforge.net/p/samtools/mailman/message/35033807/

PR:		209653
Submitted by:	cartwright@asu.edu (maintainer)
This commit is contained in:
Kurt Jaeger 2016-05-26 20:28:55 +00:00
parent 349c737413
commit 04b3bb054f
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=415914
8 changed files with 23 additions and 20 deletions
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6
biology/bcftools/Makefile
View file

@ -2,19 +2,21 @@
# $FreeBSD$ # $FreeBSD$
PORTNAME= bcftools PORTNAME= bcftools
PORTVERSION= 1.3 PORTVERSION= 1.3.1
CATEGORIES= biology CATEGORIES= biology
MAINTAINER= cartwright@asu.edu MAINTAINER= cartwright@asu.edu
COMMENT= Tools for manipulating next-generation sequencing data COMMENT= Tools for manipulating next-generation sequencing data
LICENSE= MIT LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE # LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= htslib>=1.3:biology/htslib BUILD_DEPENDS= htslib>=1.3:biology/htslib
LIB_DEPENDS= libhts.so:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib
TEST_DEPENDS= bash:shells/bash TEST_DEPENDS= bash:shells/bash
CONFLICTS_BUILD=openssl
USE_GITHUB= yes USE_GITHUB= yes
GH_ACCOUNT= samtools GH_ACCOUNT= samtools

5
biology/bcftools/distinfo
View file

@ -1,2 +1,3 @@
SHA256 (samtools-bcftools-1.3_GH0.tar.gz) = 3f4d4bf68637070cb7dbb5d5619ece7e3315727e651eab751d849085439b11d8 TIMESTAMP = 1463692643
SIZE (samtools-bcftools-1.3_GH0.tar.gz) = 943041 SHA256 (samtools-bcftools-1.3.1_GH0.tar.gz) = 99a5cc05faa974f5ddbeebf346bb51a806bdaaf8e2f6adc3bead28551983e77e
SIZE (samtools-bcftools-1.3.1_GH0.tar.gz) = 958207

1
biology/bcftools/pkg-plist
View file

@ -2,6 +2,7 @@ bin/bcftools
bin/samtools_misc/color-chrs.pl bin/samtools_misc/color-chrs.pl
bin/samtools_misc/plot-vcfstats bin/samtools_misc/plot-vcfstats
bin/samtools_misc/vcfutils.pl bin/samtools_misc/vcfutils.pl
libexec/bcftools/GTisec.so
libexec/bcftools/color-chrs.so libexec/bcftools/color-chrs.so
libexec/bcftools/counts.so libexec/bcftools/counts.so
libexec/bcftools/dosage.so libexec/bcftools/dosage.so

4
biology/htslib/Makefile
View file

@ -2,7 +2,7 @@
# $FreeBSD$ # $FreeBSD$
PORTNAME= htslib PORTNAME= htslib
PORTVERSION= 1.3 PORTVERSION= 1.3.1
CATEGORIES= biology devel CATEGORIES= biology devel
MAINTAINER= cartwright@asu.edu MAINTAINER= cartwright@asu.edu
@ -21,7 +21,7 @@ USES= autoreconf gmake perl5 shebangfix
USE_PERL5= test USE_PERL5= test
USE_LDCONFIG= yes USE_LDCONFIG= yes
GNU_CONFIGURE= 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_DEFINE= CURL
OPTIONS_DEFAULT= CURL OPTIONS_DEFAULT= CURL

5
biology/htslib/distinfo
View file

@ -1,2 +1,3 @@
SHA256 (samtools-htslib-1.3_GH0.tar.gz) = 291a54090df3bc367b509890e1cfa34d53b1ee9be42c5fa6c2b1e2ec8f8b13af TIMESTAMP = 1463688817
SIZE (samtools-htslib-1.3_GH0.tar.gz) = 1042953 SHA256 (samtools-htslib-1.3.1_GH0.tar.gz) = 3bbd04f9a0c4c301abd5d19a81920894ac2ee5e86e8aa977e8c2035e01d93ea7
SIZE (samtools-htslib-1.3.1_GH0.tar.gz) = 1065840

2
biology/samtools/Makefile
View file

@ -2,7 +2,7 @@
# $FreeBSD$ # $FreeBSD$
PORTNAME= samtools PORTNAME= samtools
PORTVERSION= 1.3 PORTVERSION= 1.3.1
CATEGORIES= biology CATEGORIES= biology
MAINTAINER= cartwright@asu.edu MAINTAINER= cartwright@asu.edu

5
biology/samtools/distinfo
View file

@ -1,2 +1,3 @@
SHA256 (samtools-samtools-1.3_GH0.tar.gz) = f1eee9a217d547d9b483098519738ef351ec454f4a85cdb1e77ae8892fe858b5 TIMESTAMP = 1463691050
SIZE (samtools-samtools-1.3_GH0.tar.gz) = 3742904 SHA256 (samtools-samtools-1.3.1_GH0.tar.gz) = 30752c7b92cd9e146f4017983b2a41beb58c8966e93572cea76a14719f95a768
SIZE (samtools-samtools-1.3.1_GH0.tar.gz) = 3757176

15
biology/samtools/files/patch-Makefile
View file

@ -1,6 +1,6 @@
--- Makefile.orig 2015-12-15 21:26:20 UTC --- Makefile.orig 2016-04-22 09:22:44 UTC
+++ Makefile +++ 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_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
bam_quickcheck.o bam_addrprg.o bam_quickcheck.o bam_addrprg.o
@ -26,7 +26,7 @@
PROGRAMS = samtools PROGRAMS = samtools
@@ -60,7 +60,6 @@ BUILT_MISC_PROGRAMS = \ @@ -59,7 +59,6 @@ BUILT_MISC_PROGRAMS = \
misc/md5fa misc/md5sum-lite misc/wgsim misc/md5fa misc/md5sum-lite misc/wgsim
MISC_PROGRAMS = \ MISC_PROGRAMS = \
@ -34,19 +34,16 @@
misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \ misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \
misc/interpolate_sam.pl misc/novo2sam.pl \ misc/interpolate_sam.pl misc/novo2sam.pl \
misc/plot-bamstats misc/psl2sam.pl \ misc/plot-bamstats misc/psl2sam.pl \
@@ -81,9 +80,9 @@ BUILT_TEST_PROGRAMS = \ @@ -82,7 +81,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS)
# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally # 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_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS)
-ALL_LIBS = -lz -ldl $(LIBS) -ALL_LIBS = -lz -ldl $(LIBS)
+ALL_LIBS = -lz $(LIBS) +ALL_LIBS = -lz $(LIBS)
# Usually config.mk and config.h are generated by running configure # Usually config.mk and config.h are generated by running configure
# or config.status, but if those aren't used create defaults here. # 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: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)