From owner-dev-commits-ports-main@freebsd.org Sun Apr 18 18:47:08 2021 Return-Path: Delivered-To: dev-commits-ports-main@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id AB3105F14DD; Sun, 18 Apr 2021 18:47:08 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4FNf7c4RmPz3w7v; Sun, 18 Apr 2021 18:47:08 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 8B94A11034; Sun, 18 Apr 2021 18:47:08 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 13IIl8Uj040294; Sun, 18 Apr 2021 18:47:08 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 13IIl8nX040293; Sun, 18 Apr 2021 18:47:08 GMT (envelope-from git) Date: Sun, 18 Apr 2021 18:47:08 GMT Message-Id: <202104181847.13IIl8nX040293@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 5164d38ee538 - main - biology/snpeff: Genetic variant annotation and effect prediction toolbox MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 5164d38ee538f6791a25b81f28a27126b90444f7 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-main@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commits to the main branch of the FreeBSD ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 18 Apr 2021 18:47:08 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=5164d38ee538f6791a25b81f28a27126b90444f7 commit 5164d38ee538f6791a25b81f28a27126b90444f7 Author: Jason W. Bacon AuthorDate: 2021-04-18 18:46:14 +0000 Commit: Jason W. Bacon 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 ${WRKSRC}/scripts/snpSift + +.include diff --git a/biology/snpeff/distinfo b/biology/snpeff/distinfo new file mode 100644 index 000000000000..895315e4a8c3 --- /dev/null +++ b/biology/snpeff/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1618353537 +SHA256 (snpEff_latest_core.zip) = 85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d +SIZE (snpEff_latest_core.zip) = 45828841 diff --git a/biology/snpeff/files/patch-scripts_snpEff b/biology/snpeff/files/patch-scripts_snpEff new file mode 100644 index 000000000000..dace484960d7 --- /dev/null +++ b/biology/snpeff/files/patch-scripts_snpEff @@ -0,0 +1,27 @@ +--- scripts/snpEff.orig 2021-04-13 22:55:13 UTC ++++ scripts/snpEff +@@ -13,9 +13,10 @@ + # Created by: Brad Chapman + #--------------------------------------------------------------------------------------------------- + +-jardir="$(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