Date: Sun, 18 Apr 2021 18:47:08 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 5164d38ee538 - main - biology/snpeff: Genetic variant annotation and effect prediction toolbox Message-ID: <202104181847.13IIl8nX040293@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=5164d38ee538f6791a25b81f28a27126b90444f7 commit 5164d38ee538f6791a25b81f28a27126b90444f7 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-04-18 18:46:14 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-04-18 18:46:29 +0000 biology/snpeff: Genetic variant annotation and effect prediction toolbox 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). --- biology/Makefile | 1 + biology/snpeff/Makefile | 41 ++++++++++++++++ biology/snpeff/distinfo | 3 ++ biology/snpeff/files/patch-scripts_snpEff | 27 +++++++++++ biology/snpeff/files/patch-scripts_snpSift | 19 ++++++++ biology/snpeff/pkg-descr | 14 ++++++ biology/snpeff/pkg-plist | 75 ++++++++++++++++++++++++++++++ 7 files changed, 180 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 40af21229bfa..7c6bfbddf1d1 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -168,6 +168,7 @@ SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman + SUBDIR += snpeff SUBDIR += spoa SUBDIR += stacks SUBDIR += star 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 ${WRKSRC}/scripts/snpSift + +.include <bsd.port.mk> diff --git a/biology/snpeff/distinfo b/biology/snpeff/distinfo new file mode 100644 index 000000000000..895315e4a8c3 --- /dev/null +++ b/biology/snpeff/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1618353537 +SHA256 (snpEff_latest_core.zip) = 85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d +SIZE (snpEff_latest_core.zip) = 45828841 diff --git a/biology/snpeff/files/patch-scripts_snpEff b/biology/snpeff/files/patch-scripts_snpEff new file mode 100644 index 000000000000..dace484960d7 --- /dev/null +++ b/biology/snpeff/files/patch-scripts_snpEff @@ -0,0 +1,27 @@ +--- scripts/snpEff.orig 2021-04-13 22:55:13 UTC ++++ scripts/snpEff +@@ -13,9 +13,10 @@ + # Created by: Brad Chapman + #--------------------------------------------------------------------------------------------------- + +-jardir="$(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
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