Date: Wed, 11 Jul 2018 21:32:39 +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: r474480 - in head/biology: . stringtie stringtie/files Message-ID: <201807112132.w6BLWd49063387@repo.freebsd.org>
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Author: yuri Date: Wed Jul 11 21:32:39 2018 New Revision: 474480 URL: https://svnweb.freebsd.org/changeset/ports/474480 Log: New port: biology/stringtie: Transcript assembly and quantification for RNA-seq PR: 229480 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp> Added: head/biology/stringtie/ head/biology/stringtie/Makefile (contents, props changed) head/biology/stringtie/distinfo (contents, props changed) head/biology/stringtie/files/ head/biology/stringtie/files/patch-Makefile (contents, props changed) head/biology/stringtie/files/patch-gclib_GIntHash.hh (contents, props changed) head/biology/stringtie/files/patch-samtools-0.1.18_Makefile (contents, props changed) head/biology/stringtie/files/patch-samtools-0.1.18_bam__aux.c (contents, props changed) head/biology/stringtie/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Wed Jul 11 21:16:26 2018 (r474479) +++ head/biology/Makefile Wed Jul 11 21:32:39 2018 (r474480) @@ -125,6 +125,7 @@ SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks + SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp Added: head/biology/stringtie/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/stringtie/Makefile Wed Jul 11 21:32:39 2018 (r474480) @@ -0,0 +1,24 @@ +# $FreeBSD$ + +PORTNAME= stringtie +DISTVERSION= 1.3.4d +CATEGORIES= biology +MASTER_SITES= http://ccb.jhu.edu/software/stringtie/dl/ + +MAINTAINER= mzaki@niid.go.jp +COMMENT= Transcript assembly and quantification for RNA-seq + +LICENSE= ART20 MIT +LICENSE_COMB= multi +LICENSE_FILE_ART20= ${WRKSRC}/LICENSE +LICENSE_FILE_MIT= ${WRKSRC}/samtools-0.1.18/COPYING + +USES= gmake +ALL_TARGET= release + +PLIST_FILES= bin/stringtie + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/stringtie ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> Added: head/biology/stringtie/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/stringtie/distinfo Wed Jul 11 21:32:39 2018 (r474480) @@ -0,0 +1,3 @@ +TIMESTAMP = 1530582079 +SHA256 (stringtie-1.3.4d.tar.gz) = b1962d0108146ce7fea39d069b5e5de918e0e21daef9e1425ec9b778094d6ae6 +SIZE (stringtie-1.3.4d.tar.gz) = 438025 Added: head/biology/stringtie/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/stringtie/files/patch-Makefile Wed Jul 11 21:32:39 2018 (r474480) @@ -0,0 +1,68 @@ +--- Makefile.orig 2018-03-06 16:29:49 UTC ++++ Makefile +@@ -6,12 +6,12 @@ GDIR :=./gclib + + INCDIRS := -I. -I${GDIR} -I${BAM} + +-CC := g++ ++CXX ?= g++ + + BASEFLAGS := -Wall -Wextra ${INCDIRS} -fsigned-char -D_FILE_OFFSET_BITS=64 \ + -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti + +-LINKER := g++ ++LINKER = ${CXX} + + LDFLAGS := -g -L${BAM} $(LDFLAGS) + +@@ -22,13 +22,13 @@ ifneq (,$(findstring nothreads,$(MAKECMD + endif + + #detect MinGW (Windows environment) +-ifneq (,$(findstring mingw,$(shell ${CC} -dumpmachine))) ++ifneq (,$(findstring mingw,$(shell ${CXX} -dumpmachine))) + WINDOWS=1 + endif + + # MinGW32 GCC 4.5 link problem fix + #ifdef WINDOWS +-ifneq (,$(findstring 4.5.,$(shell g++ -dumpversion))) ++ifneq (,$(findstring 4.5.,$(shell ${CXX} -dumpversion))) + STATIC_CLIB=1 + endif + #endif +@@ -63,7 +63,7 @@ endif + ifneq (,$(filter %release %static, $(MAKECMDGOALS))) + # -- release build + RELEASE_BUILD=1 +- CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS) -O3 ++ CFLAGS := -DNDEBUG -g $(BASEFLAGS) $(CFLAGS) + else + ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS))) + #use sanitizer in gcc 4.9+ +@@ -122,7 +122,7 @@ endif + + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CFLAGS} -c $< -o $@ + + OBJS += rlink.o tablemaker.o tmerge.o + +@@ -137,7 +137,7 @@ rlink.o : rlink.h tablemaker.h $(GDIR)/G + tmerge.o : rlink.h tmerge.h + tablemaker.o : tablemaker.h rlink.h + ${BAM}/libbam.a: +- cd ${BAM} && make lib ++ cd ${BAM} && ${MAKE} lib + stringtie: ${BAM}/libbam.a $(OBJS) stringtie.o + ${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS} + @echo +@@ -151,6 +151,6 @@ clean: + ${RM} stringtie${EXE} stringtie.o* $(OBJS) + ${RM} core.* + allclean cleanAll cleanall: +- cd ${BAM} && make clean ++ cd ${BAM} && ${MAKE} clean + ${RM} stringtie${EXE} stringtie.o* $(OBJS) + ${RM} core.* Added: head/biology/stringtie/files/patch-gclib_GIntHash.hh ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/stringtie/files/patch-gclib_GIntHash.hh Wed Jul 11 21:32:39 2018 (r474480) @@ -0,0 +1,20 @@ +--- gclib/GIntHash.hh.orig 2018-03-06 16:29:49 UTC ++++ gclib/GIntHash.hh +@@ -122,7 +122,7 @@ public: + uint32 NextKey() { + Cell* cell=ghash.NextCell(); + if (cell) return cell->key; +- else return NULL; ++ else return 0; + } + OBJ* NextValue() { + Cell* cell=ghash.NextCell(); +@@ -201,7 +201,7 @@ public: + uint32 NextKey() { + Cell* cell=ghash.NextCell(); + if (cell) return cell->key; +- else return NULL; ++ else return 0; + } + OBJ* NextValue() { + Cell* cell=ghash.NextCell(); Added: head/biology/stringtie/files/patch-samtools-0.1.18_Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/stringtie/files/patch-samtools-0.1.18_Makefile Wed Jul 11 21:32:39 2018 (r474480) @@ -0,0 +1,10 @@ +--- samtools-0.1.18/Makefile.orig 2018-03-06 16:29:49 UTC ++++ samtools-0.1.18/Makefile +@@ -1,5 +1,5 @@ +-CC= gcc +-CFLAGS= -g -Wall -fsigned-char -O2 #-m64 #-arch ppc ++CC?= gcc ++CFLAGS?= -g -Wall -fsigned-char -O2 #-m64 #-arch ppc + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 #-D_USE_KNETFILE + KNETFILE_O= knetfile.o + LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ Added: head/biology/stringtie/files/patch-samtools-0.1.18_bam__aux.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/stringtie/files/patch-samtools-0.1.18_bam__aux.c Wed Jul 11 21:32:39 2018 (r474480) @@ -0,0 +1,20 @@ +--- samtools-0.1.18/bam_aux.c.orig 2018-03-06 16:29:49 UTC ++++ samtools-0.1.18/bam_aux.c +@@ -25,7 +25,7 @@ uint8_t *bam_aux_get_core(bam1_t *b, con + return bam_aux_get(b, tag); + } + +-inline int aux_type2size(uint8_t type) ++int aux_type2size(uint8_t type) + { + switch (type) { + case 'A': case 'c': case 'C': +@@ -43,7 +43,7 @@ inline int aux_type2size(uint8_t type) + } + } + +-inline uint8_t* skip_aux(uint8_t* s) { ++uint8_t* skip_aux(uint8_t* s) { + int size = aux_type2size(*s); ++s; // skip type + uint32_t n; + switch (size) { Added: head/biology/stringtie/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/stringtie/pkg-descr Wed Jul 11 21:32:39 2018 (r474480) @@ -0,0 +1,11 @@ +StringTie is a fast and highly efficient assembler of RNA-seq alignments into +potential transcripts. The input can be the alignments of raw reads as usual; +it also accepts longer assembled sequences. The output can be processed by +downstream software including Ballgown, Cuffdiff, etc. + +Citation: +Pertea et al. (2015) StringTie enables improved reconstruction of a +transcriptome from RNA-seq reads. +Nature Biotechnology 33: 290-295 doi:10.1038/nbt.3122 + +WWW: http://www.ccb.jhu.edu/software/stringtie/
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