Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 473805) +++ head/biology/Makefile (revision 473806) @@ -1,142 +1,143 @@ # $FreeBSD$ # 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 += cytoscape 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/cytoscape/Makefile =================================================================== --- head/biology/cytoscape/Makefile (nonexistent) +++ head/biology/cytoscape/Makefile (revision 473806) @@ -0,0 +1,59 @@ +# $FreeBSD$ + +PORTNAME= cytoscape +DISTVERSION= 3.6.1 +CATEGORIES= biology java +MASTER_SITES= LOCAL/yuri/:maven \ + http://people.freebsd.org/~yuri/:maven +DISTFILES= FreeBSD-${PORTNAME}-${PORTVERSION}-maven-repository.tar.gz:maven + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Software to visualize molecular interaction networks, gene expression + +LICENSE= MIT +xLICENSE_FILE= ${WRKSRC}/license.txt + +BUILD_DEPENDS= mvn:devel/maven \ + bash:shells/bash +RUN_DEPENDS= bash:shells/bash + +USES= shebangfix +SHEBANG_FILES= gui-distribution/assembly/src/main/bin/cytoscape.sh +USE_JAVA= yes +JAVA_VERSION= 1.7+ +USE_GITHUB= yes +GH_TUPLE= ${PORTNAME}:${PORTNAME}-parent:${DISTVERSION}:p/parent \ + ${PORTNAME}:${PORTNAME}-api:${DISTVERSION}:a/api \ + ${PORTNAME}:${PORTNAME}-impl:${DISTVERSION}:i/impl \ + ${PORTNAME}:${PORTNAME}-support:${DISTVERSION}:s/support \ + ${PORTNAME}:${PORTNAME}-gui-distribution:${DISTVERSION}:g/gui-distribution \ + ${PORTNAME}:${PORTNAME}-app-template:${DISTVERSION}:d/app-developer +NO_ARCH= yes + +USER_WRKDIR= ~/.${PORTNAME} + +do-build: + @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} \ + ${LOCALBASE}/bin/mvn --offline \ + -fae install \ + -Dmaven.test.skip=true \ + -Duser.home=${WRKDIR} + +do-install: + @cd ${WRKSRC} && ${COPYTREE_SHARE} gui-distribution ${STAGEDIR}${DATADIR} + # shouldn't be needed, but the executable bit sometimes isn't set + @${CHMOD} +x ${STAGEDIR}${DATADIR}/gui-distribution/assembly/target/cytoscape/cytoscape.sh + @${CHMOD} +x ${STAGEDIR}${DATADIR}/gui-distribution/assembly/target/cytoscape/framework/bin/karaf + # create a shell executable calling the real command + @(echo "#!/bin/sh"; \ + echo ""; \ + echo "cd ${DATADIR} && JAVA_HOME=${JAVA_HOME} ./gui-distribution/assembly/target/cytoscape/cytoscape.sh \"$@\"" \ + ) > ${STAGEDIR}${PREFIX}/bin/${PORTNAME} + @${CHMOD} +x ${STAGEDIR}${PREFIX}/bin/${PORTNAME} + # redirect user data to /tmp until they fix the location so that it would write under $HOME + @${RM} -r ${STAGEDIR}${DATADIR}/gui-distribution/assembly/target/cytoscape/framework/instances + @cd ${STAGEDIR}${DATADIR}/gui-distribution/assembly/target/cytoscape/framework && ${LN} -s /tmp instances + # use the automatic plist: a few hundred files are under DATADIR + @${SETENV} ${CO_ENV} ${SH} ${SCRIPTSDIR}/check-stagedir.sh makeplist | ${GREP} -v ^\/ | ${SED} -e 's|%%DATADIR%%|share/${PORTNAME}|' > ${TMPPLIST} + +.include Property changes on: head/biology/cytoscape/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/cytoscape/distinfo =================================================================== --- head/biology/cytoscape/distinfo (nonexistent) +++ head/biology/cytoscape/distinfo (revision 473806) @@ -0,0 +1,17 @@ +TIMESTAMP = 1530603760 +SHA256 (FreeBSD-cytoscape-3.6.1-maven-repository.tar.gz) = f3e33e99168b56768d2ee854956e59bcbb888101fd518239887524d692b78f7a +SIZE (FreeBSD-cytoscape-3.6.1-maven-repository.tar.gz) = 1235655281 +SHA256 (cytoscape-cytoscape-3.6.1_GH0.tar.gz) = f172c9e459293661a83d2618da511901410336b76b0c1716697e60f821c2f150 +SIZE (cytoscape-cytoscape-3.6.1_GH0.tar.gz) = 12785 +SHA256 (cytoscape-cytoscape-parent-3.6.1_GH0.tar.gz) = 0786e8d7877fa54d2a64d65209856a4a946df4facd3cbc947e8c65d14a035084 +SIZE (cytoscape-cytoscape-parent-3.6.1_GH0.tar.gz) = 2863 +SHA256 (cytoscape-cytoscape-api-3.6.1_GH0.tar.gz) = a264a434d5942cad2ef69df7aa29fad74a6d1f11369a964d7c38462608def73b +SIZE (cytoscape-cytoscape-api-3.6.1_GH0.tar.gz) = 1731631 +SHA256 (cytoscape-cytoscape-impl-3.6.1_GH0.tar.gz) = 0fcea5a4d804972db5b0cf77174a953d22da8fed6740dbaa01754eb7aea50d21 +SIZE (cytoscape-cytoscape-impl-3.6.1_GH0.tar.gz) = 29851040 +SHA256 (cytoscape-cytoscape-support-3.6.1_GH0.tar.gz) = 3f13088c35d41fa616dc7e735469f360ee4d17b1838cde8291f88b01bacfe657 +SIZE (cytoscape-cytoscape-support-3.6.1_GH0.tar.gz) = 52940 +SHA256 (cytoscape-cytoscape-gui-distribution-3.6.1_GH0.tar.gz) = 73fb7efb51a0413252a7e9e28d4fb7e28d16eea9f60be534fd962a5e534ca72e +SIZE (cytoscape-cytoscape-gui-distribution-3.6.1_GH0.tar.gz) = 14818052 +SHA256 (cytoscape-cytoscape-app-template-3.6.1_GH0.tar.gz) = 9cf7b64a3e6effd22a20d577c7fa41b11f896e2298ef1655f2fe31c21602bce0 +SIZE (cytoscape-cytoscape-app-template-3.6.1_GH0.tar.gz) = 1887 Property changes on: head/biology/cytoscape/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/cytoscape/pkg-descr =================================================================== --- head/biology/cytoscape/pkg-descr (nonexistent) +++ head/biology/cytoscape/pkg-descr (revision 473806) @@ -0,0 +1,6 @@ +Cytoscape is an open source software platform for visualizing complex networks +and integrating these with any type of attribute data. A lot of Apps are +available for various kinds of problem domains, including bioinformatics, social +network analysis, and semantic web. + +WWW: http://www.cytoscape.org Property changes on: head/biology/cytoscape/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