Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 499591) +++ head/biology/Makefile (revision 499592) @@ -1,160 +1,161 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa 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 += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm 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 += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += molden SUBDIR += mopac 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-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 += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise .include Index: head/biology/star/Makefile =================================================================== --- head/biology/star/Makefile (nonexistent) +++ head/biology/star/Makefile (revision 499592) @@ -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 Property changes on: head/biology/star/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/star/distinfo =================================================================== --- head/biology/star/distinfo (nonexistent) +++ head/biology/star/distinfo (revision 499592) @@ -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 Property changes on: head/biology/star/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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/star/files/patch-Makefile =================================================================== --- head/biology/star/files/patch-Makefile (nonexistent) +++ head/biology/star/files/patch-Makefile (revision 499592) @@ -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 + + + ########################################################################################################## Property changes on: head/biology/star/files/patch-Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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/star/files/patch-SharedMemory.cpp =================================================================== --- head/biology/star/files/patch-SharedMemory.cpp (nonexistent) +++ head/biology/star/files/patch-SharedMemory.cpp (revision 499592) @@ -0,0 +1,11 @@ +--- SharedMemory.cpp.orig 2019-04-21 19:57:39 UTC ++++ SharedMemory.cpp +@@ -11,7 +11,7 @@ + #include + #include + +-#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 Property changes on: head/biology/star/files/patch-SharedMemory.cpp ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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/star/pkg-descr =================================================================== --- head/biology/star/pkg-descr (nonexistent) +++ head/biology/star/pkg-descr (revision 499592) @@ -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 Property changes on: head/biology/star/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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