8 files changed, 23 insertions, 20 deletions

diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile
index e0b804b87190..ddde407aa8d6 100644
--- a/biology/bcftools/Makefile
+++ b/biology/bcftools/Makefile
@@ -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
 
diff --git a/biology/bcftools/distinfo b/biology/bcftools/distinfo
index dd518aea8303..2d4c03eecc90 100644
--- a/biology/bcftools/distinfo
+++ b/biology/bcftools/distinfo
@@ -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
diff --git a/biology/bcftools/pkg-plist b/biology/bcftools/pkg-plist
index 46544ca50e9f..a005b7adb727 100644
--- a/biology/bcftools/pkg-plist
+++ b/biology/bcftools/pkg-plist
@@ -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
diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile
index c7a9feec1c20..d906a3428bd8 100644
--- a/biology/htslib/Makefile
+++ b/biology/htslib/Makefile
@@ -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
diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo
index 434c3ff8cc00..d5438781f02d 100644
--- a/biology/htslib/distinfo
+++ b/biology/htslib/distinfo
@@ -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
diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile
index 620026bdf6c7..632d0a9c001e 100644
--- a/biology/samtools/Makefile
+++ b/biology/samtools/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	samtools
-PORTVERSION=	1.3
+PORTVERSION=	1.3.1
 CATEGORIES=	biology
 
 MAINTAINER=	cartwright@asu.edu
diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo
index 4013c9dd4364..439a947c14cb 100644
--- a/biology/samtools/distinfo
+++ b/biology/samtools/distinfo
@@ -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
diff --git a/biology/samtools/files/patch-Makefile b/biology/samtools/files/patch-Makefile
index 53e049f2cf1c..eaa977f79e05 100644
--- a/biology/samtools/files/patch-Makefile
+++ b/biology/samtools/files/patch-Makefile
@@ -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)