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cufflinks: Clean up

This commit is contained in:
Jason W. Bacon 2017-09-05 15:39:02 -05:00
parent 54a3861848
commit 989b6819e5
4 changed files with 7 additions and 9 deletions
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10
cufflinks/Makefile
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@ -11,8 +11,8 @@ MASTER_SITES= http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/
MAINTAINER= dsiercks@uwm.edu
HOMEPAGE= http://port.home.page/
COMMENT= Transcript assembly, differential expression and regulation for RNA-Seq
# LICENSE=
COMMENT= Transcript assembly, differential expression, regulation for RNA-Seq
LICENSE= boost-license
USE_LANGUAGES= c c++
GNU_CONFIGURE= yes
@ -30,7 +30,6 @@ SUBST_SED.boost+= -e 's|logl|log|g'
SUBST_SED.boost+= -e 's|long double|double|g'
SUBST_SED.boost+= -e 's|Lf|lf|g'
SUBST_SED.boost+= -e 's|Lg|lg|g'
SUBST_MESSAGE.boost= "Substituting for boost"
SUBST_FILES.boost+= ${WRKSRC}/src/abundances.cpp
SUBST_FILES.boost+= ${WRKSRC}/src/abundances.h
SUBST_FILES.boost+= ${WRKSRC}/src/assemble.h
@ -60,11 +59,8 @@ SUBST_STAGE.boolint= post-patch
SUBST_FILES.boolint= ${WRKSRC}/src/rounding.h
SUBST_SED.boolint+= -e 's|int& is_up|bool\& is_up|g'
# CONFIGURE_ARGS are not linker flags. Run configure --help to see
# proper usage of --with-bam
CONFIGURE_ARGS+=--with-bam=${PREFIX}/samtools0119 --with-boost
# CONFIGURE_ARGS+=--with-bam="-L${PREFIX}/lib ${LINKER_RPATH_FLAG}${PREFIX}/lib"
CFLAGS+= -I${LOCALBASE}/include/eigen3
CFLAGS+= -I${PREFIX}/include/eigen3
LDFLAGS+= -lboost_system -lboost_iostreams -lboost_thread
PORTVERSION= 2.1.1

4
cufflinks/distinfo
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@ -4,5 +4,5 @@ SHA1 (cufflinks-2.1.1.tar.gz) = 9c5bf3d3872e8dd358ba7d7407644ab2cbbfdcb6
RMD160 (cufflinks-2.1.1.tar.gz) = 4a612f98be24d7d31520be0501f1f4bcd3e76e0f
SHA512 (cufflinks-2.1.1.tar.gz) = 3a52852d356240eeb24bfc10e449524499f03e8b908133f35e7fcb6ccb5d3566bacd99aa752082081b601fcd2872f5335473ccecb2cd1cb9a9224af41b224c29
Size (cufflinks-2.1.1.tar.gz) = 705930 bytes
SHA1 (patch-configure) = fa6121ad0abad7bfcc9cfc585b395999b107277c
SHA1 (patch-src_bundles.cpp) = d90c68a2613c42b182e5dc4250f0609e55789c5b
SHA1 (patch-configure) = 87a10d1d224f60370f6c42f901460529f57df59f
SHA1 (patch-src_bundles.cpp) = fcb5e8ba79faa1d1fdebcbe96da0fbc54d959b6e

1
cufflinks/patches/patch-configure
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@ -1,5 +1,6 @@
$NetBSD$
# Non-portable shell feature
--- configure.orig 2013-04-11 13:09:12.000000000 +0000
+++ configure
@@ -6339,7 +6339,7 @@ LDFLAGS="$LDFLAGS $EIGEN_LDFLAGS"

1
cufflinks/patches/patch-src_bundles.cpp
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@ -1,5 +1,6 @@
$NetBSD$
# Constant too big for int on some systems
--- src/bundles.cpp.orig 2013-04-04 14:41:19.000000000 +0000
+++ src/bundles.cpp
@@ -677,7 +677,7 @@ double BundleFactory::next_valid_alignme