svn commit: r502661 - in head/biology: . cufflinks cufflinks/files

[Yuri Victorovich]

Author: yuri
Date: Sat May 25 22:28:12 2019
New Revision: 502661
URL: https://svnweb.freebsd.org/changeset/ports/502661

Log:
  New port: biology/cufflinks: Cufflinks assembles transcripts, estimates their abundance, etc

Added:
  head/biology/cufflinks/
  head/biology/cufflinks/Makefile   (contents, props changed)
  head/biology/cufflinks/distinfo   (contents, props changed)
  head/biology/cufflinks/files/
  head/biology/cufflinks/files/patch-src_GBase.h   (contents, props changed)
  head/biology/cufflinks/files/patch-src_biascorrection.h   (contents, props changed)
  head/biology/cufflinks/pkg-descr   (contents, props changed)
Modified:
  head/biology/Makefile

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Sat May 25 22:05:13 2019	(r502660)
+++ head/biology/Makefile	Sat May 25 22:28:12 2019	(r502661)
@@ -22,6 +22,7 @@
     SUBDIR += clustal-omega
     SUBDIR += clustalw
     SUBDIR += consed
+    SUBDIR += cufflinks
     SUBDIR += cytoscape
     SUBDIR += ddocent
     SUBDIR += diamond

Added: head/biology/cufflinks/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/cufflinks/Makefile	Sat May 25 22:28:12 2019	(r502661)
@@ -0,0 +1,40 @@
+# $FreeBSD$
+
+PORTNAME=	cufflinks
+DISTVERSIONPREFIX=	v
+DISTVERSION=	2.2.1-83
+DISTVERSIONSUFFIX=	-gb4fa050
+CATEGORIES=	biology
+
+MAINTAINER=	yuri at FreeBSD.org
+COMMENT=	Cufflinks assembles transcripts, estimates their abundance, etc
+
+LICENSE=	BSL
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+LIB_DEPENDS=	libboost_system.so:devel/boost-libs \
+		libhts.so:biology/htslib
+
+USES=		autoreconf eigen:3 gmake python shebangfix
+SHEBANG_FILES=	src/cuffmerge
+GNU_CONFIGURE=	yes
+USE_GITHUB=	yes
+GH_ACCOUNT=	cole-trapnell-lab
+
+CXXFLAGS+=	-I${LOCALBASE}/include/eigen3
+CFLAGS+=	-I${LOCALBASE}/include/eigen3 # https://github.com/cole-trapnell-lab/cufflinks/issues/113
+
+PLIST_FILES=	bin/compress_gtf \
+		bin/cuffcompare \
+		bin/cuffdiff \
+		bin/cufflinks \
+		bin/cuffmerge \
+		bin/cuffnorm \
+		bin/cuffquant \
+		bin/gffread \
+		bin/gtf_to_sam
+
+post-patch: # https://github.com/cole-trapnell-lab/cufflinks/issues/116
+	@${GREP} -rl 'fabs(' ${WRKSRC} | ${GREP} "\.cpp$$" | ${XARGS} ${REINPLACE_CMD} 's|std::fabs(|fabs(| ; s|fabs(|::fabs(|'
+
+.include <bsd.port.mk>

Added: head/biology/cufflinks/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/cufflinks/distinfo	Sat May 25 22:28:12 2019	(r502661)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1558818522
+SHA256 (cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz) = 0b26b02c080115d4262d466503bdc43db5ff5583d8122e77355782dc7cbe0522
+SIZE (cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz) = 8804967

Added: head/biology/cufflinks/files/patch-src_GBase.h
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/cufflinks/files/patch-src_GBase.h	Sat May 25 22:28:12 2019	(r502661)
@@ -0,0 +1,10 @@
+--- src/GBase.h.orig	2019-05-25 22:08:19 UTC
++++ src/GBase.h
+@@ -1,6 +1,6 @@
+ #ifndef G_BASE_DEFINED
+ #define G_BASE_DEFINED
+-#ifndef _POSIX_SOURCE
++#if !defined(_POSIX_SOURCE) && !defined(__FreeBSD__)
+ //mostly for MinGW
+ #define _POSIX_SOURCE
+ #endif

Added: head/biology/cufflinks/files/patch-src_biascorrection.h
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/cufflinks/files/patch-src_biascorrection.h	Sat May 25 22:28:12 2019	(r502661)
@@ -0,0 +1,11 @@
+--- src/biascorrection.h.orig	2019-05-25 21:22:56 UTC
++++ src/biascorrection.h
+@@ -15,7 +15,7 @@
+ #include <vector>
+ #include <list>
+ #include <string>
+-#include <boost/tr1/unordered_map.hpp>
++#include <boost/unordered_map.hpp>
+ #include <boost/thread.hpp>
+ #include "common.h"
+ 

Added: head/biology/cufflinks/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/cufflinks/pkg-descr	Sat May 25 22:28:12 2019	(r502661)
@@ -0,0 +1,15 @@
+Cufflinks assembles transcripts, estimates their abundances, and tests for
+differential expression and regulation in RNA-Seq samples. It accepts aligned
+RNA-Seq reads and assembles the alignments into a parsimonious set of
+transcripts. Cufflinks then estimates the relative abundances of these
+transcripts based on how many reads support each one, taking into account biases
+in library preparation protocols.
+
+Cufflinks was originally developed as part of a collaborative effort between the
+Laboratory for Mathematical and Computational Biology, led by Lior Pachter at UC
+Berkeley, Steven Salzberg's computational genomics group at the Institute of
+Genetic Medicine at Johns Hopkins University, and Barbara Wold's lab at Caltech.
+The project is now maintained by Cole Trapnell's lab at the University of
+Washington.
+
+WWW: http://cole-trapnell-lab.github.io/cufflinks/