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biology/snpeff: Genetic variant annotation and effect prediction toolbox

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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).
This commit is contained in:
Jason W. Bacon 2021-04-18 13:46:14 -05:00
parent 5e8ca4f8bf
commit 5164d38ee5
7 changed files with 180 additions and 0 deletions
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1
biology/Makefile
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@ -168,6 +168,7 @@
SUBDIR += sim4 SUBDIR += sim4
SUBDIR += slclust SUBDIR += slclust
SUBDIR += smithwaterman SUBDIR += smithwaterman
SUBDIR += snpeff
SUBDIR += spoa SUBDIR += spoa
SUBDIR += stacks SUBDIR += stacks
SUBDIR += star SUBDIR += star

41
biology/snpeff/Makefile Normal file
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@ -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>

3
biology/snpeff/distinfo Normal file
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@ -0,0 +1,3 @@
TIMESTAMP = 1618353537
SHA256 (snpEff_latest_core.zip) = 85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d
SIZE (snpEff_latest_core.zip) = 45828841

27
biology/snpeff/files/patch-scripts_snpEff Normal file
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@ -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

19
biology/snpeff/files/patch-scripts_snpSift Normal file
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@ -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

14
biology/snpeff/pkg-descr Normal file
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@ -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/

75
biology/snpeff/pkg-plist Normal file
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@ -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