svn commit: r544098 - in head/biology/samtools: . files
Jason W. Bacon
jwb at FreeBSD.org
Mon Aug 3 18:22:08 UTC 2020
Author: jwb
Date: Mon Aug 3 18:22:06 2020
New Revision: 544098
URL: https://svnweb.freebsd.org/changeset/ports/544098
Log:
biology/samtools: Upgrade to 1.10
Numerous bug fixes and enhancements:
https://github.com/samtools/samtools/releases/tag/1.10
Take maintainership per ports/248089
PR: ports/248089
Modified:
head/biology/samtools/Makefile
head/biology/samtools/distinfo (contents, props changed)
head/biology/samtools/files/patch-Makefile (contents, props changed)
head/biology/samtools/files/patch-test_test.pl
head/biology/samtools/pkg-plist (contents, props changed)
Modified: head/biology/samtools/Makefile
==============================================================================
--- head/biology/samtools/Makefile Mon Aug 3 18:21:18 2020 (r544097)
+++ head/biology/samtools/Makefile Mon Aug 3 18:22:06 2020 (r544098)
@@ -2,29 +2,26 @@
# $FreeBSD$
PORTNAME= samtools
-DISTVERSION= 1.9
-PORTREVISION= 1
+DISTVERSION= 1.10
CATEGORIES= biology
-MAINTAINER= cartwright at asu.edu
+MAINTAINER= jwb at FreeBSD.org
COMMENT= Tools for manipulating next-generation sequencing data
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
-BUILD_DEPENDS= htslib>=1.6:biology/htslib
-LIB_DEPENDS= libhts.so:biology/htslib
+LIB_DEPENDS= libhts.so.3:biology/htslib
TEST_DEPENDS= bash:shells/bash
-USES= autoreconf gmake localbase ncurses \
- perl5 python:env shebangfix
+USES= autoreconf gmake localbase ncurses perl5 python:env shebangfix
USE_GITHUB= yes
USE_PERL5= test
GNU_CONFIGURE= yes
SUB_FILES= pkg-message
-SHEBANG_FILES= misc/*.pl misc/*.py misc/plot-bamstats test/test.pl
+SHEBANG_FILES= misc/*.pl misc/plot-bamstats test/test.pl
TEST_TARGET= test
Modified: head/biology/samtools/distinfo
==============================================================================
--- head/biology/samtools/distinfo Mon Aug 3 18:21:18 2020 (r544097)
+++ head/biology/samtools/distinfo Mon Aug 3 18:22:06 2020 (r544098)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1532906637
-SHA256 (samtools-samtools-1.9_GH0.tar.gz) = 211600bd180d01030b3fe25baa7ae1c105106bed6c3f8d993f41dd278d44c637
-SIZE (samtools-samtools-1.9_GH0.tar.gz) = 4098992
+TIMESTAMP = 1595117115
+SHA256 (samtools-samtools-1.10_GH0.tar.gz) = 382843e85fdb55868cebaaf2585c43776762d099581341b5803677de5ed117a9
+SIZE (samtools-samtools-1.10_GH0.tar.gz) = 4457760
Modified: head/biology/samtools/files/patch-Makefile
==============================================================================
--- head/biology/samtools/files/patch-Makefile Mon Aug 3 18:21:18 2020 (r544097)
+++ head/biology/samtools/files/patch-Makefile Mon Aug 3 18:22:06 2020 (r544098)
@@ -1,11 +1,30 @@
---- Makefile.orig 2017-09-28 11:12:01 UTC
+--- Makefile.orig 2019-12-06 16:40:42 UTC
+++ Makefile
-@@ -40,23 +40,22 @@ 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 bam_markdup.o
+@@ -21,12 +21,12 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+-CC = gcc
+-AR = ar
+-CPPFLAGS =
++CC ?= gcc
++AR ?= ar
++# CPPFLAGS =
+ #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
+-CFLAGS = -g -Wall -O2
+-LDFLAGS =
++CFLAGS ?= -g -Wall -O2
++# LDFLAGS =
+ LIBS =
+
+ LZ4DIR = ./lz4
+@@ -47,23 +47,24 @@ AOBJS= bam_index.o bam_plcmd.o sam_view.o bam_fas
+ bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o
+ LZ4OBJS = $(LZ4DIR)/lz4.o
+
-prefix = /usr/local
-+prefix = ${PREFIX}
++PREFIX ?= /usr/local
++prefix = $(PREFIX)
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
datarootdir = $(prefix)/share
@@ -17,6 +36,7 @@
-misc_bindir = $(bindir)
+misc_bindir = $(bindir)/samtools_misc
++# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
MKDIR_P = mkdir -p
-INSTALL = install -p
-INSTALL_DATA = $(INSTALL) -m 644
Modified: head/biology/samtools/files/patch-test_test.pl
==============================================================================
--- head/biology/samtools/files/patch-test_test.pl Mon Aug 3 18:21:18 2020 (r544097)
+++ head/biology/samtools/files/patch-test_test.pl Mon Aug 3 18:22:06 2020 (r544098)
@@ -1,20 +1,20 @@
---- test/test.pl.orig 2017-10-18 06:08:39 UTC
+--- test/test.pl.orig 2020-07-21 20:48:50 UTC
+++ test/test.pl
-@@ -636,7 +636,7 @@ sub test_usage
+@@ -907,7 +907,7 @@ sub test_usage
my $command = $args{cmd};
my $commandpath = $$opts{bin}."/".$command;
my ($ret,$out,$err) = _cmd("$commandpath $args{redirection}");
- if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
-+ if ( $err =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
++ if ( $err =~ m/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
my @sections = ($err =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
-@@ -694,7 +694,7 @@ sub test_usage_subcommand
+@@ -965,7 +965,7 @@ sub test_usage_subcommand
my $commandpath = $$opts{bin}."/".$command;
my ($ret,$out,$err) = _cmd("$commandpath $subcommand $args{redirection}");
- if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
-+ if ( $err =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
++ if ( $err =~ m/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
if ( $err =~ m/not.*implemented/is ) { failed($opts,msg=>$test,reason=>"subcommand indicates it is not implemented",expect_fail=>1); return; }
Modified: head/biology/samtools/pkg-plist
==============================================================================
--- head/biology/samtools/pkg-plist Mon Aug 3 18:21:18 2020 (r544097)
+++ head/biology/samtools/pkg-plist Mon Aug 3 18:22:06 2020 (r544098)
@@ -15,9 +15,38 @@ bin/samtools_misc/sam2vcf.pl
bin/samtools_misc/samtools.pl
bin/samtools_misc/seq_cache_populate.pl
bin/samtools_misc/soap2sam.pl
-bin/samtools_misc/varfilter.py
bin/samtools_misc/wgsim
bin/samtools_misc/wgsim_eval.pl
bin/samtools_misc/zoom2sam.pl
+man/man1/samtools-addreplacerg.1.gz
+man/man1/samtools-bedcov.1.gz
+man/man1/samtools-calmd.1.gz
+man/man1/samtools-cat.1.gz
+man/man1/samtools-collate.1.gz
+man/man1/samtools-depad.1.gz
+man/man1/samtools-depth.1.gz
+man/man1/samtools-dict.1.gz
+man/man1/samtools-faidx.1.gz
+man/man1/samtools-fasta.1.gz
+man/man1/samtools-fastq.1.gz
+man/man1/samtools-fixmate.1.gz
+man/man1/samtools-flags.1.gz
+man/man1/samtools-flagstat.1.gz
+man/man1/samtools-fqidx.1.gz
+man/man1/samtools-idxstats.1.gz
+man/man1/samtools-index.1.gz
+man/man1/samtools-markdup.1.gz
+man/man1/samtools-merge.1.gz
+man/man1/samtools-mpileup.1.gz
+man/man1/samtools-phase.1.gz
+man/man1/samtools-quickcheck.1.gz
+man/man1/samtools-reheader.1.gz
+man/man1/samtools-rmdup.1.gz
+man/man1/samtools-sort.1.gz
+man/man1/samtools-split.1.gz
+man/man1/samtools-stats.1.gz
+man/man1/samtools-targetcut.1.gz
+man/man1/samtools-tview.1.gz
+man/man1/samtools-view.1.gz
man/man1/samtools.1.gz
man/man1/wgsim.1.gz
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