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-rw-r--r--biology/Makefile1
-rw-r--r--biology/snpeff/Makefile41
-rw-r--r--biology/snpeff/distinfo3
-rw-r--r--biology/snpeff/files/patch-scripts_snpEff27
-rw-r--r--biology/snpeff/files/patch-scripts_snpSift19
-rw-r--r--biology/snpeff/pkg-descr14
-rw-r--r--biology/snpeff/pkg-plist75
7 files changed, 180 insertions, 0 deletions
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
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-25 03:46:58 +0000