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Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/ cufflinks-2.2.1 cufflinks-2.2.1 | tail -n 1 as wip/cufflinks-2.2.1.

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Thu May 12 21:59:52 2016 -0500
Changeset:	878045f761226ecd0506ed27773a07bdbcf3a6ec

Added Files:
	cufflinks-2.2.1/DESCR
	cufflinks-2.2.1/Makefile
	cufflinks-2.2.1/PLIST
	cufflinks-2.2.1/TODO
	cufflinks-2.2.1/distinfo
	cufflinks-2.2.1/patches/patch-configure
	cufflinks-2.2.1/patches/patch-src_bundles.cpp

Log Message:
Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/cufflinks-2.2.1
cufflinks-2.2.1 | tail -n 1 as wip/cufflinks-2.2.1.

Latest not-so-stable version.

Cufflinks assembles transcripts, estimates their abundances, and tests for
differential expression and regulation in RNA-Seq samples.

WWW: http://port.home.page/

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=878045f761226ecd0506ed27773a07bdbcf3a6ec

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 cufflinks-2.2.1/DESCR                         |  4 ++
 cufflinks-2.2.1/Makefile                      | 53 +++++++++++++++++++++++++++
 cufflinks-2.2.1/PLIST                         | 10 +++++
 cufflinks-2.2.1/TODO                          |  1 +
 cufflinks-2.2.1/distinfo                      |  8 ++++
 cufflinks-2.2.1/patches/patch-configure       | 13 +++++++
 cufflinks-2.2.1/patches/patch-src_bundles.cpp | 13 +++++++
 7 files changed, 102 insertions(+)

diffs:
diff --git a/cufflinks-2.2.1/DESCR b/cufflinks-2.2.1/DESCR
new file mode 100644
index 0000000..4eecdb7
--- /dev/null
+++ b/cufflinks-2.2.1/DESCR
@@ -0,0 +1,4 @@
+Cufflinks assembles transcripts, estimates their abundances, and tests for
+differential expression and regulation in RNA-Seq samples.
+
+WWW: http://port.home.page/
diff --git a/cufflinks-2.2.1/Makefile b/cufflinks-2.2.1/Makefile
new file mode 100644
index 0000000..d6ce283
--- /dev/null
+++ b/cufflinks-2.2.1/Makefile
@@ -0,0 +1,53 @@
+# $NetBSD: Makefile,v 1.1 2014/09/04 21:51:02 outpaddling Exp $
+
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+# This version is known for frequent crashes
+# FIXME: boost problem and hackaround:
+# https://svn.boost.org/trac/boost/query?status=!closed&page=3&order=summary&row=description: #9331
+
+DISTNAME=	cufflinks-2.2.1
+CATEGORIES=	biology
+MASTER_SITES=	http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/
+
+MAINTAINER=	jwbacon%tds.net@localhost
+
+COMMENT=	RNA transcript assembly, differential expression/regulation
+# LICENSE=
+
+USE_LANGUAGES=	c c++
+GNU_CONFIGURE=	yes
+CONFIGURE_ARGS+=	--with-bam=${PREFIX}/samtools0119
+
+# Darwin
+CFLAGS+=	-I${LOCALBASE}/include/eigen3
+# These are getting left out on CentOS and Darwin in spite of buildlink
+LDFLAGS+=	-L${PREFIX}/lib -lboost_thread -lboost_system -lboost_serialization
+
+# Darwin i386 Snow Leopard doesn't support /bin/arch or /usr/bin/arch -k
+SUBST_CLASSES+=		arch
+SUBST_STAGE.arch=	post-patch
+SUBST_FILES.arch=	configure
+SUBST_SED.arch=		's|arch -k|arch|g'
+
+# Allow compiling on i386
+SUBST_CLASSES+=		cflags
+SUBST_STAGE.cflags=	post-patch
+SUBST_FILES.cflags=	configure
+SUBST_SED.cflags=	's|-arch x86_64||g'
+
+SUBST_CLASSES+=		ldouble
+SUBST_STAGE.ldouble=	post-patch
+SUBST_FILES.ldouble=	${WRKSRC}/src/*.cpp ${WRKSRC}/src/*.h
+SUBST_SED.ldouble=	-e 's|logl|log|g' -e 's|long double|double|g'
+
+.include "../../wip/samtools0119/buildlink3.mk"
+.include "../../devel/boost-libs/buildlink3.mk"
+.include "../../devel/boost-headers/buildlink3.mk"
+.include "../../devel/boost-jam/buildlink3.mk"
+# CentOS can't find libbam without this.  samtools buildlink issue?
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../math/eigen3/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/cufflinks-2.2.1/PLIST b/cufflinks-2.2.1/PLIST
new file mode 100644
index 0000000..f9111cd
--- /dev/null
+++ b/cufflinks-2.2.1/PLIST
@@ -0,0 +1,10 @@
+@comment $NetBSD: PLIST,v 1.1 2014/09/04 21:51:02 outpaddling Exp $
+bin/compress_gtf
+bin/cuffcompare
+bin/cuffdiff
+bin/cufflinks
+bin/cuffmerge
+bin/cuffnorm
+bin/cuffquant
+bin/gffread
+bin/gtf_to_sam
diff --git a/cufflinks-2.2.1/TODO b/cufflinks-2.2.1/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/cufflinks-2.2.1/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/cufflinks-2.2.1/distinfo b/cufflinks-2.2.1/distinfo
new file mode 100644
index 0000000..dd71512
--- /dev/null
+++ b/cufflinks-2.2.1/distinfo
@@ -0,0 +1,8 @@
+$NetBSD: distinfo,v 1.1 2014/09/04 21:51:02 outpaddling Exp $
+
+SHA1 (cufflinks-2.2.1.tar.gz) = 2b1b3a8f12cd2821ffc74ffbdd55cb329f37cbbb
+RMD160 (cufflinks-2.2.1.tar.gz) = 6378571ecb06971d1dff5b6ef81a55b36a8be498
+SHA512 (cufflinks-2.2.1.tar.gz) = 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b
+Size (cufflinks-2.2.1.tar.gz) = 766280 bytes
+SHA1 (patch-configure) = 24e592c47e814f5c355a2351752473507ed9fca5
+SHA1 (patch-src_bundles.cpp) = 4240e40a3f16223e868a421248972f057b3a74f4
diff --git a/cufflinks-2.2.1/patches/patch-configure b/cufflinks-2.2.1/patches/patch-configure
new file mode 100644
index 0000000..ba09a47
--- /dev/null
+++ b/cufflinks-2.2.1/patches/patch-configure
@@ -0,0 +1,13 @@
+$NetBSD$
+
+--- configure.orig	2015-09-30 01:19:17.827123473 +0000
++++ configure
+@@ -7592,7 +7592,7 @@ LDFLAGS="$LDFLAGS $EIGEN_LDFLAGS"
+ export LDFLAGS
+ export EIGEN_CPPFLAGS
+ 
+-if test "$succeeded" == "yes" ; then
++if test "$succeeded" = "yes" ; then
+ 
+ 
+ cat >>confdefs.h <<\_ACEOF
diff --git a/cufflinks-2.2.1/patches/patch-src_bundles.cpp b/cufflinks-2.2.1/patches/patch-src_bundles.cpp
new file mode 100644
index 0000000..a3bc281
--- /dev/null
+++ b/cufflinks-2.2.1/patches/patch-src_bundles.cpp
@@ -0,0 +1,13 @@
+$NetBSD: patch-src_bundles.cpp,v 1.1 2014/09/04 21:51:02 outpaddling Exp $
+
+--- src/bundles.cpp.orig	2014-03-24 21:54:47.000000000 +0000
++++ src/bundles.cpp
+@@ -698,7 +698,7 @@ double BundleFactory::next_valid_alignme
+         if (!_hit_fac->get_hit_from_buf(hit_buf, tmp, false))
+             continue;
+         
+-		if (tmp.ref_id() == 12638153115695167477)  // corresponds to SAM "*" under FNV hash. unaligned read record 
++		if (tmp.ref_id() == 12638153115695167477ULL)  // corresponds to SAM "*" under FNV hash. unaligned read record 
+             continue;
+         
+ 		raw_mass += tmp.mass();
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