diff options
| -rw-r--r-- | biology/bowtie/Makefile | 12 | ||||
| -rw-r--r-- | biology/bowtie/files/patch-ebwt.h | 11 |
2 files changed, 17 insertions, 6 deletions
diff --git a/biology/bowtie/Makefile b/biology/bowtie/Makefile index 8d486190a122..015dc7462aca 100644 --- a/biology/bowtie/Makefile +++ b/biology/bowtie/Makefile @@ -1,9 +1,9 @@ # $FreeBSD$ PORTNAME= bowtie -PORTVERSION= 1.1.2 -PORTREVISION= 6 DISTVERSIONPREFIX= v +DISTVERSION= 1.1.2 +PORTREVISION= 7 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -13,15 +13,15 @@ LICENSE= ART10 # May also work on other 64-bit platforms, but untested ONLY_FOR_ARCHS= amd64 + # FIXME: bowtie-align intermittently dumps core when compiled with clang # GCC 4.2 does not provide good performance -USE_GCC= yes USES= gmake perl5 python:run shebangfix +USE_GCC= yes USE_PERL5= run -SHEBANG_FILES= scripts/*.pl bowtie bowtie-build \ - bowtie-inspect - USE_GITHUB= yes + +SHEBANG_FILES= scripts/*.pl bowtie bowtie-build bowtie-inspect GH_ACCOUNT= BenLangmead OPTIONS_DEFINE= DOCS diff --git a/biology/bowtie/files/patch-ebwt.h b/biology/bowtie/files/patch-ebwt.h new file mode 100644 index 000000000000..4272bbd8303c --- /dev/null +++ b/biology/bowtie/files/patch-ebwt.h @@ -0,0 +1,11 @@ +--- ebwt.h.orig 2018-11-03 20:51:56 UTC ++++ ebwt.h +@@ -860,7 +860,7 @@ public: + TIndexOffU* ftab() const { return _ftab; } + TIndexOffU* eftab() const { return _eftab; } + TIndexOffU* offs() const { return _offs; } +- uint32_t* isa() const { return _isa; } /* check */ ++ uint32_t* isa() const { return (uint32_t)_isa; } /* check */ + TIndexOffU* plen() const { return _plen; } + TIndexOffU* rstarts() const { return _rstarts; } + uint8_t* ebwt() const { return _ebwt; } |