Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 473355) +++ head/biology/Makefile (revision 473356) @@ -1,141 +1,142 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += clustalx SUBDIR += consed SUBDIR += ddocent SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa 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-toolkit SUBDIR += ngs-sdk SUBDIR += njplot SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene 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 += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-macs2 SUBDIR += py-orange3-bioinformatics SUBDIR += py-pysam 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 += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcftools SUBDIR += vcflib SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/igv/Makefile =================================================================== --- head/biology/igv/Makefile (nonexistent) +++ head/biology/igv/Makefile (revision 473356) @@ -0,0 +1,46 @@ +# $FreeBSD$ + +PORTNAME= igv +DISTVERSIONPREFIX= v +DISTVERSION= 2.4.10 +CATEGORIES= biology java +MASTER_SITES= http://www.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img +DISTFILES= tools.png:img +DIST_SUBDIR= ${PORTNAME}-${DISTVERSION} +EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Visualization tool for genomic datasets + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/license.txt + +BUILD_DEPENDS= openjfx8-devel>0:java/openjfx8-devel +RUN_DEPENDS= openjfx8-devel>0:java/openjfx8-devel + +USES= gettext-runtime +USE_GITHUB= yes +GH_ACCOUNT= igvteam +USE_JAVA= yes +USE_ANT= yes +NO_ARCH= yes + +SUB_FILES= ${PORTNAME}.sh + +DESKTOP_ENTRIES="IGV" "Integrative Genomics Viewer" "${PREFIX}/share/pixmaps/igv.xpm" "${PORTNAME}" \ + "Biology;Science;" true + +PLIST_FILES= bin/${PORTNAME} \ + ${JAVAJARDIR}/batik-codec__V1.7.jar \ + ${JAVAJARDIR}/goby-io-igv__V1.0.jar \ + ${JAVAJARDIR}/${PORTNAME}.jar \ + share/pixmaps/igv.png + +do-install: + ${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME} + ${INSTALL_DATA} ${WRKSRC}/${PORTNAME}.jar ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_DATA} ${WRKSRC}/batik-codec__V1.7.jar ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_DATA} ${WRKSRC}/goby-io-igv__V1.0.jar ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/tools.png ${STAGEDIR}${PREFIX}/share/pixmaps/${PORTNAME}.png + +.include Property changes on: head/biology/igv/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/igv/distinfo =================================================================== --- head/biology/igv/distinfo (nonexistent) +++ head/biology/igv/distinfo (revision 473356) @@ -0,0 +1,5 @@ +TIMESTAMP = 1529969906 +SHA256 (igv-2.4.10/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c +SIZE (igv-2.4.10/tools.png) = 5139 +SHA256 (igv-2.4.10/igvteam-igv-v2.4.10_GH0.tar.gz) = 2547050f768384ea14f88962476c6935115e6b2e35322874e4a93c6da7194e73 +SIZE (igv-2.4.10/igvteam-igv-v2.4.10_GH0.tar.gz) = 152822902 Property changes on: head/biology/igv/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/igv/files/igv.sh.in =================================================================== --- head/biology/igv/files/igv.sh.in (nonexistent) +++ head/biology/igv/files/igv.sh.in (revision 473356) @@ -0,0 +1,9 @@ +#!/bin/sh +LANG=C +# phymem=$(free -m | awk '/^Mem:/{print $2}') +#igvmem=$(($phymem / 3)) +# ARGS=-Xmx${igvmem}m +java $ARGS \ + -Dapple.laf.useScreenMenuBar=true \ + -Djava.net.preferIPv4Stack=true \ + -jar %%JAVAJARDIR%%/igv.jar Property changes on: head/biology/igv/files/igv.sh.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/igv/files/patch-build.xml =================================================================== --- head/biology/igv/files/patch-build.xml (nonexistent) +++ head/biology/igv/files/patch-build.xml (revision 473356) @@ -0,0 +1,10 @@ +--- build.xml.orig 2018-06-25 21:00:29 UTC ++++ build.xml +@@ -177,6 +177,7 @@ + + + ++ + + + Property changes on: head/biology/igv/files/patch-build.xml ___________________________________________________________________ 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/igv/pkg-descr =================================================================== --- head/biology/igv/pkg-descr (nonexistent) +++ head/biology/igv/pkg-descr (revision 473356) @@ -0,0 +1,6 @@ +The Integrative Genomics Viewer (IGV) is a high-performance visualization tool +for interactive exploration of large, integrated genomic datasets. It supports +a wide variety of data types, including array-based and next-generation sequence +data, and genomic annotations. + +WWW: https://software.broadinstitute.org/software/igv/ Property changes on: head/biology/igv/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