diff --git a/biology/Makefile b/biology/Makefile index f02dc903a129..60ab10072e29 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,205 +1,206 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bbmap SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc SUBDIR += bioparser SUBDIR += biosoup SUBDIR += biostar-tools SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += edlib SUBDIR += emboss + SUBDIR += erminej 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 += gcta SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan 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 += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += mmseqs2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-entrez-direct SUBDIR += ncbi-toolkit SUBDIR += ncbi-vdb SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-DB-EMBL SUBDIR += p5-Bio-DB-NCBIHelper 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-Bio-Variation SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbseqan SUBDIR += peak-classifier SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phyml SUBDIR += picard-tools SUBDIR += plink SUBDIR += pooler SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-bigwig SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-gffutils SUBDIR += py-goatools SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-resdk SUBDIR += py-scikit-bio SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler SUBDIR += readseq SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables SUBDIR += rubygem-bio-old-biofetch-emulator SUBDIR += rubygem-bio-shell SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqan3 SUBDIR += seqio SUBDIR += seqkit SUBDIR += seqtk SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += snpeff SUBDIR += spoa SUBDIR += sra-tools SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += taxonkit SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ucsc-userapps SUBDIR += ugene SUBDIR += unikmer SUBDIR += vcf-split SUBDIR += vcf2hap SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wise .include diff --git a/biology/erminej/Makefile b/biology/erminej/Makefile new file mode 100644 index 000000000000..39c19e7d2a25 --- /dev/null +++ b/biology/erminej/Makefile @@ -0,0 +1,29 @@ +PORTNAME= erminej +DISTVERSION= 3.2 +CATEGORIES= biology java +MASTER_SITES= http://home.pavlab.msl.ubc.ca/ermineJ/distributions/ +DISTNAME= ermineJ-${DISTVERSION}-generic-bundle + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Analyses of gene sets such as gene expression profiling studies + +LICENSE= APACHE20 +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +USES= zip +USE_JAVA= yes + +WRKSRC= ${WRKDIR}/ermineJ-${DISTVERSION} +NO_BUILD= yes +NO_ARCH= yes + +SUB_FILES= ermineJ +SUB_LIST= JAVA_HOME=${JAVA_HOME} + +do-install: + cd ${WRKSRC}/lib && ${COPYTREE_SHARE} . \ + ${STAGEDIR}${JAVAJARDIR}/${PORTNAME} + ${INSTALL_SCRIPT} ${WRKDIR}/ermineJ ${STAGEDIR}${PREFIX}/bin + ${INSTALL_DATA} ${WRKSRC}/bin/forehead.conf ${STAGEDIR}${PREFIX}/etc + +.include diff --git a/biology/erminej/distinfo b/biology/erminej/distinfo new file mode 100644 index 000000000000..8e979af904bd --- /dev/null +++ b/biology/erminej/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1625698692 +SHA256 (ermineJ-3.2-generic-bundle.zip) = 6e711b100e7619863ad2730714cdfa466115b563c146cb20a30488780504d5ac +SIZE (ermineJ-3.2-generic-bundle.zip) = 14314004 diff --git a/biology/erminej/files/ermineJ.in b/biology/erminej/files/ermineJ.in new file mode 100755 index 000000000000..f53de8eb4354 --- /dev/null +++ b/biology/erminej/files/ermineJ.in @@ -0,0 +1,17 @@ +#!/bin/sh + +ERMINEJ_HOME=%%JAVAJARDIR%%/erminej +ERMINEJ_ETC=%%PREFIX%%/etc +JAVA_HOME=%%JAVA_HOME%% +JAVACMD=$JAVA_HOME/bin/java + +MAIN_CLASS=com.werken.forehead.Forehead + +set -x +"$JAVACMD" \ + -Xmx3g \ + -Djavax.xml.parsers.SAXParserFactory=org.apache.xerces.jaxp.SAXParserFactoryImpl \ + -classpath "$ERMINEJ_HOME/forehead.jar" \ + "-Dforehead.conf.file=$ERMINEJ_ETC/forehead.conf" \ + "-DermineJ.home=$ERMINEJ_HOME" \ + $MAIN_CLASS "$@" diff --git a/biology/erminej/files/patch-bin_forehead.conf b/biology/erminej/files/patch-bin_forehead.conf new file mode 100644 index 000000000000..38a18bcef949 --- /dev/null +++ b/biology/erminej/files/patch-bin_forehead.conf @@ -0,0 +1,18 @@ +--- bin/forehead.conf.orig 2021-07-08 00:06:39 UTC ++++ bin/forehead.conf +@@ -7,12 +7,12 @@ + =[root.ermineJCmd] ubic.erminej.ErmineJCli + + [root] +- ${ermineJ.home}/lib/*.jar ++ ${ermineJ.home}/*.jar + + [root.ermineJ] +- ${ermineJ.home}/lib/*.jar ++ ${ermineJ.home}/*.jar + + + [root.ermineJCmd] +- ${ermineJ.home}/lib/*.jar ++ ${ermineJ.home}/*.jar + diff --git a/biology/erminej/pkg-descr b/biology/erminej/pkg-descr new file mode 100644 index 000000000000..94ccbf50a01b --- /dev/null +++ b/biology/erminej/pkg-descr @@ -0,0 +1,8 @@ +ErmineJ performs analyses of gene sets in high-throughput genomics data such as +gene expression profiling studies. A typical goal is to determine whether +particular biological pathways are "doing something interesting" in an +experiment that generates long lists of candidates. The software is designed to +be used by biologists with little or no informatics background (but if you do, +you might be interested in the CLI or the R support). + +WWW: https://erminej.msl.ubc.ca/ diff --git a/biology/erminej/pkg-plist b/biology/erminej/pkg-plist new file mode 100644 index 000000000000..132aa436cbd7 --- /dev/null +++ b/biology/erminej/pkg-plist @@ -0,0 +1,31 @@ +bin/ermineJ +etc/forehead.conf +%%JAVAJARDIR%%/erminej/antlr.jar +%%JAVAJARDIR%%/erminej/baseCode.jar +%%JAVAJARDIR%%/erminej/colt.jar +%%JAVAJARDIR%%/erminej/commons-beanutils.jar +%%JAVAJARDIR%%/erminej/commons-cli.jar +%%JAVAJARDIR%%/erminej/commons-collections.jar +%%JAVAJARDIR%%/erminej/commons-configuration.jar +%%JAVAJARDIR%%/erminej/commons-io.jar +%%JAVAJARDIR%%/erminej/commons-lang3.jar +%%JAVAJARDIR%%/erminej/commons-logging.jar +%%JAVAJARDIR%%/erminej/commons-math3.jar +%%JAVAJARDIR%%/erminej/commons-net.jar +%%JAVAJARDIR%%/erminej/ermineJ.jar +%%JAVAJARDIR%%/erminej/forehead.jar +%%JAVAJARDIR%%/erminej/gemma-core.jar +%%JAVAJARDIR%%/erminej/gemma-gsec.jar +%%JAVAJARDIR%%/erminej/javax.activation-api.jar +%%JAVAJARDIR%%/erminej/jaxb-api.jar +%%JAVAJARDIR%%/erminej/jcl-over-slf4j.jar +%%JAVAJARDIR%%/erminej/jcommon.jar +%%JAVAJARDIR%%/erminej/jfreechart.jar +%%JAVAJARDIR%%/erminej/jsontools-core.jar +%%JAVAJARDIR%%/erminej/log4j.jar +%%JAVAJARDIR%%/erminej/mtj.jar +%%JAVAJARDIR%%/erminej/opencsv.jar +%%JAVAJARDIR%%/erminej/slf4j-api.jar +%%JAVAJARDIR%%/erminej/slf4j-log4j12.jar +%%JAVAJARDIR%%/erminej/xercesImpl.jar +%%JAVAJARDIR%%/erminej/xml-apis.jar