svn commit: r502661 - in head/biology: . cufflinks cufflinks/files
Yuri Victorovich
yuri at FreeBSD.org
Sat May 25 22:28:14 UTC 2019
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/
More information about the svn-ports-all
mailing list