Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 506416) +++ head/biology/Makefile (revision 506417) @@ -1,171 +1,172 @@ # $FreeBSD$ # 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 += 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-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 += 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/libbigwig/Makefile =================================================================== --- head/biology/libbigwig/Makefile (nonexistent) +++ head/biology/libbigwig/Makefile (revision 506417) @@ -0,0 +1,33 @@ +# $FreeBSD$ + +PORTNAME= libbigwig +DISTVERSION= 0.4.4 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= C library for handling bigWig files (containing genomic data) + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libcurl.so:ftp/curl + +USES= gmake localbase:ldflags +USE_GITHUB= yes +GH_ACCOUNT= dpryan79 +GH_PROJECT= libBigWig +USE_LDCONFIG= yes + +MAKE_ARGS= LDFLAGS=-L${LOCALBASE}/lib + +PLIST_FILES= include/bigWig.h \ + include/bigWigIO.h \ + include/bwCommon.h \ + include/bwValues.h \ + lib/libBigWig.a \ + lib/libBigWig.so + +post-stage: + @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libBigWig.so + +.include Property changes on: head/biology/libbigwig/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/libbigwig/distinfo =================================================================== --- head/biology/libbigwig/distinfo (nonexistent) +++ head/biology/libbigwig/distinfo (revision 506417) @@ -0,0 +1,3 @@ +TIMESTAMP = 1562863376 +SHA256 (dpryan79-libBigWig-0.4.4_GH0.tar.gz) = 43a2298b2ebadc48103447a3bb4426df1b38d1bec5fa564e50ed2f00cc060478 +SIZE (dpryan79-libBigWig-0.4.4_GH0.tar.gz) = 272926 Property changes on: head/biology/libbigwig/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/libbigwig/files/patch-Makefile =================================================================== --- head/biology/libbigwig/files/patch-Makefile (nonexistent) +++ head/biology/libbigwig/files/patch-Makefile (revision 506417) @@ -0,0 +1,14 @@ +--- Makefile.orig 2019-07-11 16:45:26 UTC ++++ Makefile +@@ -71,7 +71,7 @@ clean: + rm -f *.o libBigWig.a libBigWig.so *.pico test/testLocal test/testRemote test/testWrite test/exampleWrite test/testRemoteManyContigs test/testBigBed test/testIterator example_output.bw + + install: libBigWig.a libBigWig.so +- install -d $(prefix)/lib $(prefix)/include +- install libBigWig.a $(prefix)/lib +- install libBigWig.so $(prefix)/lib +- install *.h $(prefix)/include ++ install -d $(prefix)/lib $(DESTDIR)$(prefix)/include ++ install libBigWig.a $(DESTDIR)$(prefix)/lib ++ install libBigWig.so $(DESTDIR)$(prefix)/lib ++ install *.h $(DESTDIR)$(prefix)/include Property changes on: head/biology/libbigwig/files/patch-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/libbigwig/pkg-descr =================================================================== --- head/biology/libbigwig/pkg-descr (nonexistent) +++ head/biology/libbigwig/pkg-descr (revision 506417) @@ -0,0 +1,3 @@ +A C library for reading/parsing local and remote bigWig and bigBed files. + +WWW: https://github.com/dpryan79/libBigWig Property changes on: head/biology/libbigwig/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