Attachment 180156 Details for Bug 216619 – Unified diff

[patch] Unified diff

bowtie2.diff (text/plain), 3.49 KB, created by Jason W. Bacon on 2017-02-20 03:57:01 UTC

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Creator: Jason W. Bacon

Created: 2017-02-20 03:57:01 UTC

Size: 3.49 KB

patch

obsolete

>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/bowtie2/Makefile /usr/wip/biology/bowtie2/Makefile
>--- /usr/ports/biology/bowtie2/Makefile	2016-12-20 11:01:27.000000000 -0600
>+++ /usr/wip/biology/bowtie2/Makefile	2017-02-19 19:01:19.058678000 -0600
>@@ -2,7 +2,7 @@
> # $FreeBSD: head/biology/bowtie2/Makefile 429003 2016-12-20 17:01:27Z jrm $
> 
> PORTNAME=	bowtie2
>-PORTVERSION=	2.2.9
>+PORTVERSION=	2.3.0
> DISTVERSIONPREFIX=	v
> CATEGORIES=	biology
> 
>@@ -12,6 +12,8 @@
> LICENSE=	GPLv3+
> LICENSE_FILE=	${WRKSRC}/LICENSE
> 
>+LIB_DEPENDS+=	libtbb.so:devel/tbb
>+
> # May also work on other 64-bit platforms, but untested
> ONLY_FOR_ARCHS=	amd64
> USES=		gmake perl5 python shebangfix
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/bowtie2/distinfo /usr/wip/biology/bowtie2/distinfo
>--- /usr/ports/biology/bowtie2/distinfo	2016-12-20 11:01:27.000000000 -0600
>+++ /usr/wip/biology/bowtie2/distinfo	2017-02-19 19:01:19.059241000 -0600
>@@ -1,3 +1,3 @@
>-TIMESTAMP = 1475861880
>-SHA256 (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = af940f77fc36aabea90d3d865724fd7ec7e250788d2d2f793c45c713d16ae5ee
>-SIZE (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = 5815106
>+TIMESTAMP = 1487550143
>+SHA256 (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 9804fddf36233f3f92c11e2250224de3395790cf35c8280c66387075df078221
>+SIZE (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 5810016
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/bowtie2/files/patch-Makefile /usr/wip/biology/bowtie2/files/patch-Makefile
>--- /usr/ports/biology/bowtie2/files/patch-Makefile	2016-03-23 06:22:39.000000000 -0500
>+++ /usr/wip/biology/bowtie2/files/patch-Makefile	2017-02-19 19:01:19.059795000 -0600
>@@ -1,5 +1,5 @@
>---- Makefile.orig	2016-02-11 17:20:57 UTC
>-+++ Makefile
>+--- Makefile.orig	2016-12-30 09:40:06.000000000 -0600
>++++ Makefile	2017-02-19 18:55:16.371000000 -0600
> @@ -21,8 +21,8 @@
>  # Makefile for bowtie, bowtie2-build, bowtie2-inspect
>  #
>@@ -11,7 +11,34 @@
>  
>  INC =
>  GCC_PREFIX = $(shell dirname `which gcc`)
>-@@ -169,7 +169,7 @@ SSE_FLAG=-msse2 
>+@@ -62,6 +62,8 @@ ifeq (1, $(POPCNT_CAPABILITY))
>+     INC += -I third_party
>+ endif
>+ 
>++INC += -I ${LOCALBASE}/include
>++
>+ MM_DEF =
>+ 
>+ ifeq (1,$(BOWTIE_MM))
>+@@ -75,7 +77,7 @@ ifeq (1,$(BOWTIE_SHARED_MEM))
>+ endif
>+ 
>+ PTHREAD_PKG =
>+-PTHREAD_LIB =
>++PTHREAD_LIB = 
>+ 
>+ #if we're not using TBB, then we can't use queuing locks
>+ ifeq (1,$(NO_TBB))
>+@@ -94,7 +96,7 @@ endif
>+ 
>+ #default is to use Intel TBB
>+ ifneq (1,$(NO_TBB))
>+-	LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
>++	LIBS = $(PTHREAD_LIB) -L${LOCALBASE}/lib -ltbb -ltbbmalloc
>+ 	override EXTRA_FLAGS += -DWITH_TBB
>+ else
>+ 	LIBS = $(PTHREAD_LIB)
>+@@ -185,7 +187,7 @@ SSE_FLAG=-msse2
>  
>  DEBUG_FLAGS    = -O0 -g3 -m64 $(SSE_FLAG)
>  DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/bowtie2/files/patch-aligner__result.cpp /usr/wip/biology/bowtie2/files/patch-aligner__result.cpp
>--- /usr/ports/biology/bowtie2/files/patch-aligner__result.cpp	1969-12-31 18:00:00.000000000 -0600
>+++ /usr/wip/biology/bowtie2/files/patch-aligner__result.cpp	2017-02-19 19:01:19.060354000 -0600
>@@ -0,0 +1,11 @@
>+--- aligner_result.cpp.orig	2017-02-19 18:40:54.398991000 -0600
>++++ aligner_result.cpp	2017-02-19 18:41:14.093250000 -0600
>+@@ -1130,7 +1130,7 @@ bool AlnFlags::printYF(BTString& o, bool
>+ 	else if(!nfilt_  ) flag = "NS";
>+ 	else if(!scfilt_ ) flag = "SC";
>+ 	else if(!qcfilt_ ) flag = "QC";
>+-	if(flag > 0) {
>++	if(*flag != '\0') {
>+ 		if(!first) o.append('\t');
>+ 		o.append("YF:Z:");
>+ 		o.append(flag);

Flags:

jwb: maintainer-approval+

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Attachments on bug 216619: 180156