Date: Sun, 21 Apr 2019 20:30:56 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r499592 - in head/biology: . star star/files Message-ID: <201904212030.x3LKUu72062589@repo.freebsd.org>
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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@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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