Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 512996) +++ head/biology/Makefile (revision 512997) @@ -1,174 +1,175 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += consed SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gemma SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm SUBDIR += haplohseq SUBDIR += hhsuite SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-xenaPython SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp + SUBDIR += tophat SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += wise .include Index: head/biology/tophat/Makefile =================================================================== --- head/biology/tophat/Makefile (nonexistent) +++ head/biology/tophat/Makefile (revision 512997) @@ -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 Property changes on: head/biology/tophat/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/tophat/distinfo =================================================================== --- head/biology/tophat/distinfo (nonexistent) +++ head/biology/tophat/distinfo (revision 512997) @@ -0,0 +1,3 @@ +TIMESTAMP = 1522620646 +SHA256 (tophat-2.1.1.tar.gz) = 37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5 +SIZE (tophat-2.1.1.tar.gz) = 2259554 Property changes on: head/biology/tophat/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/tophat/files/patch-configure =================================================================== --- head/biology/tophat/files/patch-configure (nonexistent) +++ head/biology/tophat/files/patch-configure (revision 512997) @@ -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 $srcdir && pwd`" != "`pwd`"; then Property changes on: head/biology/tophat/files/patch-configure ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/tophat/files/patch-src-samtools-0.1.18-Makefile =================================================================== --- head/biology/tophat/files/patch-src-samtools-0.1.18-Makefile (nonexistent) +++ head/biology/tophat/files/patch-src-samtools-0.1.18-Makefile (revision 512997) @@ -0,0 +1,25 @@ +--- src/samtools-0.1.18/Makefile.orig 2016-02-14 18:21:17 UTC ++++ src/samtools-0.1.18/Makefile +@@ -1,5 +1,10 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc ++CC?= gcc ++CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc ++CC?= gcc ++CFLAGS?= -g -Wall -O2 ++# Link fails with clang on inlined functions with no -O ++CFLAGS+= -O ++RANLIB?= /usr/bin/ranlib + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 + KNETFILE_O= knetfile.o + LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ +@@ -38,7 +43,8 @@ all:$(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) Property changes on: head/biology/tophat/files/patch-src-samtools-0.1.18-Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/tophat/files/patch-src_Makefile.in =================================================================== --- head/biology/tophat/files/patch-src_Makefile.in (nonexistent) +++ head/biology/tophat/files/patch-src_Makefile.in (revision 512997) @@ -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) Property changes on: head/biology/tophat/files/patch-src_Makefile.in ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/tophat/files/tophat-test =================================================================== --- head/biology/tophat/files/tophat-test (nonexistent) +++ head/biology/tophat/files/tophat-test (revision 512997) @@ -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 Property changes on: head/biology/tophat/files/tophat-test ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/tophat/pkg-descr =================================================================== --- head/biology/tophat/pkg-descr (nonexistent) +++ head/biology/tophat/pkg-descr (revision 512997) @@ -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 Property changes on: head/biology/tophat/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/tophat/pkg-plist =================================================================== --- head/biology/tophat/pkg-plist (nonexistent) +++ head/biology/tophat/pkg-plist (revision 512997) @@ -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 Property changes on: head/biology/tophat/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property