Date: Fri, 27 Sep 2019 00:49:49 +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: r512997 - in head/biology: . tophat tophat/files Message-ID: <201909270049.x8R0nnks086801@repo.freebsd.org>
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Author: jwb Date: Fri Sep 27 00:49:48 2019 New Revision: 512997 URL: https://svnweb.freebsd.org/changeset/ports/512997 Log: biology/tophat: Fast splice junction mapper for RNA-Seq reads TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. Note: TopHat has been Superseded by HISAT2 and is no longer maintained upstream. This port is provided mainly for revisiting old studies where TopHat was used. Added: head/biology/tophat/ head/biology/tophat/Makefile (contents, props changed) head/biology/tophat/distinfo (contents, props changed) head/biology/tophat/files/ head/biology/tophat/files/patch-configure (contents, props changed) head/biology/tophat/files/patch-src-samtools-0.1.18-Makefile (contents, props changed) head/biology/tophat/files/patch-src_Makefile.in (contents, props changed) head/biology/tophat/files/tophat-test (contents, props changed) head/biology/tophat/pkg-descr (contents, props changed) head/biology/tophat/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri Sep 27 00:38:02 2019 (r512996) +++ head/biology/Makefile Fri Sep 27 00:49:48 2019 (r512997) @@ -158,6 +158,7 @@ SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp + SUBDIR += tophat SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap Added: head/biology/tophat/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tophat/Makefile Fri Sep 27 00:49:48 2019 (r512997) @@ -0,0 +1,34 @@ +# $FreeBSD$ + +PORTNAME= tophat +DISTVERSION= 2.1.1 +CATEGORIES= biology python +MASTER_SITES= http://ccb.jhu.edu/software/tophat/downloads/ + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Fast splice junction mapper for RNA-Seq reads + +LICENSE= BSL +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libboost_iostreams.so:devel/boost-libs +RUN_DEPENDS= bowtie2:biology/bowtie2 + +USES= gmake python:2.7 shebangfix + +SHEBANG_FILES= src/contig_to_chr_coords \ + src/bed_to_juncs \ + src/sra_to_solid \ + src/tophat-fusion-post \ + src/tophat.py \ + src/tophat2.sh + +GNU_CONFIGURE= yes +CFLAGS+= -Wno-unused +INSTALL_TARGET= install-strip +MAKE_JOBS_UNSAFE= yes + +post-install: + ${INSTALL_SCRIPT} ${FILESDIR}/tophat-test ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> Added: head/biology/tophat/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tophat/distinfo Fri Sep 27 00:49:48 2019 (r512997) @@ -0,0 +1,3 @@ +TIMESTAMP = 1522620646 +SHA256 (tophat-2.1.1.tar.gz) = 37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5 +SIZE (tophat-2.1.1.tar.gz) = 2259554 Added: head/biology/tophat/files/patch-configure ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tophat/files/patch-configure Fri Sep 27 00:49:48 2019 (r512997) @@ -0,0 +1,22 @@ +--- configure.orig 2016-02-24 02:55:11 UTC ++++ configure +@@ -6886,7 +6886,7 @@ case $host_os in *\ *) host_os=`echo "$h + # set CFLAGS and CXXFLAGS + #user_CFLAGS="${CXXFLAGS}" + user_CFLAGS=${CFLAGS} +-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++generic_CFLAGS="-Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" + ext_CFLAGS="" + debug_CFLAGS="" + user_LDFLAGS="$LDFLAGS" +@@ -6922,8 +6922,8 @@ else + fi + + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}" +-CXXFLAGS="$CFLAGS" +-CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2" ++CXXFLAGS="-std=gnu++98 $CFLAGS" ++CXXFLAGS="-I./SeqAn-1.4.2 $CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS" + LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS" + + if test "`cd $srcdir && pwd`" != "`pwd`"; then Added: head/biology/tophat/files/patch-src-samtools-0.1.18-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tophat/files/patch-src-samtools-0.1.18-Makefile Fri Sep 27 00:49:48 2019 (r512997) @@ -0,0 +1,25 @@ +--- src/samtools-0.1.18/Makefile.orig 2016-02-14 18:21:17 UTC ++++ src/samtools-0.1.18/Makefile +@@ -1,5 +1,10 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc ++CC?= gcc ++CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc ++CC?= gcc ++CFLAGS?= -g -Wall -O2 ++# Link fails with clang on inlined functions with no -O ++CFLAGS+= -O ++RANLIB?= /usr/bin/ranlib + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 + KNETFILE_O= knetfile.o + LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ +@@ -38,7 +43,8 @@ all:$(PROG) + lib:libbam.a + + libbam.a:$(LOBJS) +- $(AR) -csru $@ $(LOBJS) ++ $(AR) cr $@ $(LOBJS) ++ $(RANLIB) $@ + + samtools_0.1.18:lib-recur $(AOBJS) + $(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf -lm -lz #$(LIBCURSES) Added: head/biology/tophat/files/patch-src_Makefile.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tophat/files/patch-src_Makefile.in Fri Sep 27 00:49:48 2019 (r512997) @@ -0,0 +1,51 @@ +--- src/Makefile.in.orig 2016-02-24 03:08:32 UTC ++++ src/Makefile.in +@@ -1207,10 +1207,15 @@ libgc.a: $(libgc_a_OBJECTS) $(libgc_a_DE + -rm -f libgc.a + $(libgc_a_AR) libgc.a $(libgc_a_OBJECTS) $(libgc_a_LIBADD) + $(RANLIB) libgc.a ++ ++# $(SAMLIB) and $(SAMPROG) are being mysteriously deleted sometime after they ++# are copied to src. The cp below is a hack to allow the port to build. + libtophat.a: $(libtophat_a_OBJECTS) $(libtophat_a_DEPENDENCIES) $(EXTRA_libtophat_a_DEPENDENCIES) + -rm -f libtophat.a + $(libtophat_a_AR) libtophat.a $(libtophat_a_OBJECTS) $(libtophat_a_LIBADD) + $(RANLIB) libtophat.a ++ cp $(SAMDIR)/$(SAMLIB) $(SAMDIR)/$(SAMPROG) . ++ + install-binPROGRAMS: $(bin_PROGRAMS) + @$(NORMAL_INSTALL) + @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \ +@@ -1281,9 +1286,11 @@ prep_reads$(EXEEXT): $(prep_reads_OBJECT + sam_juncs$(EXEEXT): $(sam_juncs_OBJECTS) $(sam_juncs_DEPENDENCIES) $(EXTRA_sam_juncs_DEPENDENCIES) + @rm -f sam_juncs$(EXEEXT) + $(sam_juncs_LINK) $(sam_juncs_OBJECTS) $(sam_juncs_LDADD) $(LIBS) ++ + samtools_0.1.18$(EXEEXT): $(samtools_0_1_18_OBJECTS) $(samtools_0_1_18_DEPENDENCIES) $(EXTRA_samtools_0_1_18_DEPENDENCIES) +- @rm -f samtools_0.1.18$(EXEEXT) +- $(LINK) $(samtools_0_1_18_OBJECTS) $(samtools_0_1_18_LDADD) $(LIBS) ++ #rm -f samtools_0.1.18$(EXEEXT) ++ #$(LINK) $(samtools_0_1_18_OBJECTS) $(samtools_0_1_18_LDADD) $(LIBS) ++ + segment_juncs$(EXEEXT): $(segment_juncs_OBJECTS) $(segment_juncs_DEPENDENCIES) $(EXTRA_segment_juncs_DEPENDENCIES) + @rm -f segment_juncs$(EXEEXT) + $(segment_juncs_LINK) $(segment_juncs_OBJECTS) $(segment_juncs_LDADD) $(LIBS) +@@ -1658,7 +1665,7 @@ uninstall-am: uninstall-binPROGRAMS unin + + + clean-local: +- cd $(SAMDIR) && make clean ++ cd $(SAMDIR) && ${MAKE} clean + + tophat2: tophat2.sh + cp tophat2.sh tophat2 && chmod 755 tophat2 +@@ -1669,7 +1676,8 @@ tophat: tophat.py + $(SAMPROG): $(SAMLIB) + + $(SAMLIB): +- cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) .. ++ cd $(SAMDIR) && ${MAKE} $(SAMPROG) ++ cp $(SAMDIR)/$(SAMLIB) $(SAMDIR)/$(SAMPROG) . + + install-data-hook: + cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir) Added: head/biology/tophat/files/tophat-test ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tophat/files/tophat-test Fri Sep 27 00:49:48 2019 (r512997) @@ -0,0 +1,16 @@ +#!/bin/sh -e + +if [ ! -e test_data.tar.gz ]; then + fetch https://ccb.jhu.edu/software/tophat/downloads/test_data.tar.gz +fi +if [ -e test_data ]; then + cat << EOM + +test_data already exists. Remove it or run $0 from a different directory. + +EOM + exit 1 +fi +tar zxvf test_data.tar.gz +cd test_data +tophat -r 20 test_ref reads_1.fq reads_2.fq Added: head/biology/tophat/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tophat/pkg-descr Fri Sep 27 00:49:48 2019 (r512997) @@ -0,0 +1,11 @@ +TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq +reads to mammalian-sized genomes using the ultra high-throughput short read +aligner Bowtie, and then analyzes the mapping results to identify splice +junctions between exons. + +Note: + +TopHat has been Superseded by HISAT2 and is no longer maintained upstream. +This port is provided mainly for revisiting old studies where TopHat was used. + +WWW: http://ccb.jhu.edu/software/tophat/index.shtml Added: head/biology/tophat/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tophat/pkg-plist Fri Sep 27 00:49:48 2019 (r512997) @@ -0,0 +1,29 @@ +bin/bam2fastx +bin/bam_merge +bin/bed_to_juncs +bin/contig_to_chr_coords +bin/fix_map_ordering +bin/gtf_juncs +bin/gtf_to_fasta +bin/intervaltree/__init__.py +bin/intervaltree/interval.py +bin/intervaltree/intervaltree.py +bin/intervaltree/node.py +bin/juncs_db +bin/long_spanning_reads +bin/map2gtf +bin/prep_reads +bin/sam_juncs +bin/samtools_0.1.18 +bin/segment_juncs +bin/sortedcontainers/__init__.py +bin/sortedcontainers/sorteddict.py +bin/sortedcontainers/sortedlist.py +bin/sortedcontainers/sortedlistwithkey.py +bin/sortedcontainers/sortedset.py +bin/sra_to_solid +bin/tophat +bin/tophat-fusion-post +bin/tophat-test +bin/tophat2 +bin/tophat_reports
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