svn commit: r499592 - in head/biology: . star star/files
Jason W. Bacon
jwb at FreeBSD.org
Sun Apr 21 20:30:58 UTC 2019
Author: jwb
Date: Sun Apr 21 20:30:55 2019
New Revision: 499592
URL: https://svnweb.freebsd.org/changeset/ports/499592
Log:
biology/star: Spliced Transcripts Alignment to a Reference
STAR is an extremely fast RNA-seq aligner, an alternative to tophat2,
hisat2, bowtie, subread, etc.
Added:
head/biology/star/
head/biology/star/Makefile (contents, props changed)
head/biology/star/distinfo (contents, props changed)
head/biology/star/files/
head/biology/star/files/patch-Makefile (contents, props changed)
head/biology/star/files/patch-SharedMemory.cpp (contents, props changed)
head/biology/star/pkg-descr (contents, props changed)
Modified:
head/biology/Makefile
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Sun Apr 21 20:05:54 2019 (r499591)
+++ head/biology/Makefile Sun Apr 21 20:30:55 2019 (r499592)
@@ -143,6 +143,7 @@
SUBDIR += slclust
SUBDIR += smithwaterman
SUBDIR += stacks
+ SUBDIR += star
SUBDIR += stringtie
SUBDIR += tRNAscan-SE
SUBDIR += t_coffee
Added: head/biology/star/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/star/Makefile Sun Apr 21 20:30:55 2019 (r499592)
@@ -0,0 +1,27 @@
+# $FreeBSD$
+
+PORTNAME= STAR
+DISTVERSION= 2.7.0f
+CATEGORIES= biology
+
+MAINTAINER= jwb at FreeBSD.org
+COMMENT= Spliced Transcripts Alignment to a Reference
+
+LICENSE= GPLv3
+LICENSE_FILE= ${WRKDIR}/STAR-${DISTVERSION}/LICENSE
+
+# 64-bit only, needs 16+ GiB RAM for typical eukaryotic genome
+NOT_FOR_ARCHS= i386 powerpc
+
+USES= compiler:openmp gmake
+USE_GITHUB= yes
+GH_ACCOUNT= alexdobin
+
+WRKSRC_SUBDIR= source
+
+PLIST_FILES= bin/STAR
+
+do-install:
+ ${INSTALL_PROGRAM} ${WRKSRC}/STAR ${STAGEDIR}${PREFIX}/bin
+
+.include <bsd.port.mk>
Added: head/biology/star/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/star/distinfo Sun Apr 21 20:30:55 2019 (r499592)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1555876360
+SHA256 (alexdobin-STAR-2.7.0f_GH0.tar.gz) = daead0a87b259e6311f48f31ccaab5bd53ef1da9d6e5cd7210e0d714b7e23204
+SIZE (alexdobin-STAR-2.7.0f_GH0.tar.gz) = 8061887
Added: head/biology/star/files/patch-Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/star/files/patch-Makefile Sun Apr 21 20:30:55 2019 (r499592)
@@ -0,0 +1,17 @@
+--- Makefile.orig 2019-03-28 20:48:16 UTC
++++ Makefile
+@@ -20,11 +20,11 @@ LDFLAGS_gdb := $(LDFLAGS_shared)
+
+ COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
+
+-CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE)
+-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
++CXXFLAGS_common := -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE)
++CXXFLAGS_main += $(CXXFLAGS_common)
+ CXXFLAGS_gdb := -O0 -g $(CXXFLAGS_common)
+
+-CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS)
++CFLAGS += -Wall -Wextra
+
+
+ ##########################################################################################################
Added: head/biology/star/files/patch-SharedMemory.cpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/star/files/patch-SharedMemory.cpp Sun Apr 21 20:30:55 2019 (r499592)
@@ -0,0 +1,11 @@
+--- SharedMemory.cpp.orig 2019-04-21 19:57:39 UTC
++++ SharedMemory.cpp
+@@ -11,7 +11,7 @@
+ #include <semaphore.h>
+ #include <errno.h>
+
+-#ifdef COMPILE_FOR_MAC
++#if defined(COMPILE_FOR_MAC) || defined(__FreeBSD__)
+ //some Mac's idiosyncrasies: standard SHM libraries are very old and missing some definitions
+ #define SHM_NORESERVE 0
+ #endif
Added: head/biology/star/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/star/pkg-descr Sun Apr 21 20:30:55 2019 (r499592)
@@ -0,0 +1,11 @@
+STAR (Spliced Transcripts Alignment to a Reference) aims to achieve accurate
+alignment of high-throughput RNA-seq data.
+
+STAR is based on a previously undescribed RNA-seq alignment algorithm that uses
+sequential maximum mappable seed search in uncompressed suffix arrays followed
+by seed clustering and stitching procedure. STAR outperforms other aligners by
+a factor of >50 in mapping speed, aligning to the human genome 550 million 2 x
+76 bp paired-end reads per hour on a modest 12-core server, while at the same
+time improving alignment sensitivity and precision
+
+WWW: https://github.com/alexdobin/STAR
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