Date: Sat, 25 May 2019 22:28:12 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r502661 - in head/biology: . cufflinks cufflinks/files Message-ID: <201905252228.x4PMSCQ5037667@repo.freebsd.org>
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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@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/
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