diff --git a/biology/Makefile b/biology/Makefile index 40af21229bfa..7c6bfbddf1d1 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,193 +1,194 @@ 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 += 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 += 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 += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit 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 += 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-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-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 += seqio SUBDIR += seqkit SUBDIR += seqtk SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman + SUBDIR += snpeff SUBDIR += spoa SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcf-split SUBDIR += vcf2hap SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wise .include diff --git a/biology/snpeff/Makefile b/biology/snpeff/Makefile new file mode 100644 index 000000000000..3973e9a9a792 --- /dev/null +++ b/biology/snpeff/Makefile @@ -0,0 +1,41 @@ +PORTNAME= snpeff +DISTVERSION= 5.0 +CATEGORIES= biology java python +MASTER_SITES= https://snpeff.blob.core.windows.net/versions/ +DISTNAME= snpEff_latest_core + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Genetic variant annotation and effect prediction toolbox + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE.md + +RUN_DEPENDS= bash:shells/bash + +USES= python:3.6+ shebangfix zip +USE_JAVA= yes + +JAVA_VERSION= 12+ +SHEBANG_FILES= scripts/* scripts/gsa/* + +NO_BUILD= yes +NO_ARCH= yes +WRKSRC= ${WRKDIR}/snpEff + +LIBEXEC_DIR= ${PREFIX}/libexec/snpeff + +do-install: + ${MKDIR} ${STAGEDIR}${JAVAJARDIR}/snpeff + ${MKDIR} ${STAGEDIR}${LIBEXEC_DIR} + ${INSTALL_SCRIPT} ${WRKSRC}/scripts/snpEff ${STAGEDIR}${PREFIX}/bin + ${INSTALL_SCRIPT} ${WRKSRC}/scripts/snpSift ${STAGEDIR}${PREFIX}/bin + ${INSTALL_DATA} ${WRKSRC}/*.jar ${STAGEDIR}${JAVAJARDIR}/snpeff + ${INSTALL_DATA} ${WRKSRC}/*.config ${STAGEDIR}${JAVAJARDIR}/snpeff + cd ${WRKSRC}/scripts && ${COPYTREE_BIN} . ${STAGEDIR}${LIBEXEC_DIR} + +pre-configure: + ${REINPLACE_CMD} -e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g' \ + -e 's|%%PREFIX%%|${PREFIX}|g' \ + ${WRKSRC}/scripts/snpEff ${WRKSRC}/scripts/snpSift + +.include diff --git a/biology/snpeff/distinfo b/biology/snpeff/distinfo new file mode 100644 index 000000000000..895315e4a8c3 --- /dev/null +++ b/biology/snpeff/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1618353537 +SHA256 (snpEff_latest_core.zip) = 85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d +SIZE (snpEff_latest_core.zip) = 45828841 diff --git a/biology/snpeff/files/patch-scripts_snpEff b/biology/snpeff/files/patch-scripts_snpEff new file mode 100644 index 000000000000..dace484960d7 --- /dev/null +++ b/biology/snpeff/files/patch-scripts_snpEff @@ -0,0 +1,27 @@ +--- scripts/snpEff.orig 2021-04-13 22:55:13 UTC ++++ scripts/snpEff +@@ -13,9 +13,10 @@ + # Created by: Brad Chapman + #--------------------------------------------------------------------------------------------------- + +-jardir="$(cd "$(dirname "$0")" && cd ".." && pwd -P)" ++jardir=%%JAVAJARDIR%%/snpeff ++userdir=~/snpEff ++JAVA_HOME=%%PREFIX%%/openjdk12 + +-java=java + if [ -e "$JAVA_HOME/bin/java" ] + then + java="$JAVA_HOME/bin/java" +@@ -43,8 +44,9 @@ if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" + fi + if [[ "$pass_args" != "" && ! "$pass_args" =~ "-c " ]]; then +- pass_args="$pass_args -c ${jardir}/snpEff.config" ++ pass_args="$pass_args -c ${userdir}/snpEff.config" + fi + ++mkdir -p ~/snpEff ++cp ${jardir}/*.config ~/snpEff + exec $java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/snpEff.jar $pass_args +-exit diff --git a/biology/snpeff/files/patch-scripts_snpSift b/biology/snpeff/files/patch-scripts_snpSift new file mode 100644 index 000000000000..838875a344f8 --- /dev/null +++ b/biology/snpeff/files/patch-scripts_snpSift @@ -0,0 +1,19 @@ +--- scripts/snpSift.orig 2021-04-13 22:40:00 UTC ++++ scripts/snpSift +@@ -13,9 +13,9 @@ + # Created by: Brad Chapman + #--------------------------------------------------------------------------------------------------- + +-jardir="$(cd "$(dirname "$0")" && cd ".." && pwd -P)" ++jardir=%%JAVAJARDIR%%/snpeff ++JAVA_HOME=%%PREFIX%%/openjdk12 + +-java=java + if [ -e "$JAVA_HOME/bin/java" ] + then + java="$JAVA_HOME/bin/java" +@@ -44,4 +44,3 @@ if [ "$jvm_mem_opts" == "" ]; then + fi + + exec $java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/SnpSift.jar $pass_args +-exit diff --git a/biology/snpeff/pkg-descr b/biology/snpeff/pkg-descr new file mode 100644 index 000000000000..cf47db97eb96 --- /dev/null +++ b/biology/snpeff/pkg-descr @@ -0,0 +1,14 @@ +Genetic variant annotation and functional effect prediction toolbox. It +annotates and predicts the effects of genetic variants on genes and proteins +(such as amino acid changes). + +Features: + + Supports over 38,000 genomes + Standard ANN annotation format + Cancer variants analysis + GATK compatible (-o gatk) + HGVS notation + Sequence Ontology standardized terms + +WWW: http://snpeff.sourceforge.net/ diff --git a/biology/snpeff/pkg-plist b/biology/snpeff/pkg-plist new file mode 100644 index 000000000000..a004332b0b41 --- /dev/null +++ b/biology/snpeff/pkg-plist @@ -0,0 +1,75 @@ +bin/snpEff +bin/snpSift +libexec/snpeff/1kg.sh +libexec/snpeff/annotate_demo.sh +libexec/snpeff/annotate_demo_GATK.sh +libexec/snpeff/bedEffOnePerLine.pl +libexec/snpeff/buildDbNcbi.sh +libexec/snpeff/cgShore.pl +libexec/snpeff/cgShore.sh +libexec/snpeff/countColumns.py +libexec/snpeff/db.pl +libexec/snpeff/extractSequences.pl +libexec/snpeff/fasta2tab.pl +libexec/snpeff/fastaSample.pl +libexec/snpeff/fastaSplit.pl +libexec/snpeff/fastqSplit.pl +libexec/snpeff/filterBy.py +libexec/snpeff/gffRemovePhase.pl +libexec/snpeff/gsa/bayesFactor_correction_scoreCount.r +libexec/snpeff/gsa/bayesFactor_correction_scoreCount.sh +libexec/snpeff/gsa/bayesFactor_correction_scoreCount_max10.sh +libexec/snpeff/gsa/checkGeneNames.py +libexec/snpeff/gsa/create_sets.bds +libexec/snpeff/gsa/geneSetOverlap.py +libexec/snpeff/gsa/geneSetOverlap.sort.txt +libexec/snpeff/gsa/geneSetsGtex.py +libexec/snpeff/gsa/pvalue_correction_scoreCount.r +libexec/snpeff/gsa/pvalue_correction_scoreCount.sh +libexec/snpeff/gsa/pvalue_correction_scoreCount_min10.sh +libexec/snpeff/isutf8.py +libexec/snpeff/join.pl +libexec/snpeff/joinSnpEff.pl +libexec/snpeff/make_and_commit_docs.sh +libexec/snpeff/make_dbNSFP.sh +libexec/snpeff/nextProt_filter.pl +libexec/snpeff/ped2vcf.py +libexec/snpeff/plot.pl +libexec/snpeff/plotHistogram.pl +libexec/snpeff/plotLabel.pl +libexec/snpeff/plotMA.pl +libexec/snpeff/plotQQ.pl +libexec/snpeff/plotQQsubsample.pl +libexec/snpeff/plotSmoothScatter.pl +libexec/snpeff/plotXY.pl +libexec/snpeff/queue.pl +libexec/snpeff/sam2fastq.pl +libexec/snpeff/sample.pl +libexec/snpeff/snpEff +libexec/snpeff/snpEff.bak +libexec/snpeff/snpEff.orig +libexec/snpeff/snpSift +libexec/snpeff/snpSift.orig +libexec/snpeff/snpSift_filter_sample_to_number.pl +libexec/snpeff/sortLine.py +libexec/snpeff/splitChr.pl +libexec/snpeff/statsNum.pl +libexec/snpeff/swapCols.pl +libexec/snpeff/transpose.pl +libexec/snpeff/txt2fa.pl +libexec/snpeff/txt2vcf.py +libexec/snpeff/uniqCount.pl +libexec/snpeff/uniqCut.pl +libexec/snpeff/vcfAnnFirst.py +libexec/snpeff/vcfBareBones.pl +libexec/snpeff/vcfEffHighest.ORI.py +libexec/snpeff/vcfEffOnePerLine.pl +libexec/snpeff/vcfFilterSamples.pl +libexec/snpeff/vcfInfoOnePerLine.pl +libexec/snpeff/vcfOnlyAlts.pl +libexec/snpeff/vcfReduceGenotypes.pl +libexec/snpeff/vcfRefCorrect.py +libexec/snpeff/wigSplit.pl +%%JAVAJARDIR%%/snpeff/SnpSift.jar +%%JAVAJARDIR%%/snpeff/snpEff.config +%%JAVAJARDIR%%/snpeff/snpEff.jar