Mercurial > repos > jjohnson > snpeff_with_dep
changeset 14:ef4598ea7179
Add SnpSift dependency
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 21 Sep 2012 16:00:25 -0500 |
| parents | d57983929080 |
| children | bd23bbee9883 |
| files | snpEff.xml snpEff_download.xml snpSift_annotate.xml snpSift_caseControl.xml snpSift_filter.xml snpSift_int.xml tool_dependencies.xml |
| diffstat | 7 files changed, 19 insertions(+), 10 deletions(-) [+] |
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--- a/snpEff.xml Fri Sep 21 15:16:49 2012 -0500 +++ b/snpEff.xml Fri Sep 21 16:00:25 2012 -0500 @@ -9,7 +9,7 @@ <requirement type="package" version="3.0">snpEff</requirement> <requirement type="set_environment">JAVA_JAR_PATH </requirement> </requirements> - <command>java -Xmx6G -jar $JAVA_JAR_PATH/snpEff.jar eff -c $JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> + <command>java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> <inputs> <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
--- a/snpEff_download.xml Fri Sep 21 15:16:49 2012 -0500 +++ b/snpEff_download.xml Fri Sep 21 16:00:25 2012 -0500 @@ -4,7 +4,7 @@ <requirement type="package" version="3.0">snpEff</requirement> <requirement type="set_environment">JAVA_JAR_PATH </requirement> </requirements> - <command>java -jar $JAVA_JAR_PATH/snpEff.jar download -c $JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> + <command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> <inputs> <param name="genomeVersion" type="select" label="Genome"> <option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option>
--- a/snpSift_annotate.xml Fri Sep 21 15:16:49 2012 -0500 +++ b/snpSift_annotate.xml Fri Sep 21 16:00:25 2012 -0500 @@ -5,10 +5,10 @@ You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) --> <requirements> - <requirement type="package" version="3.0">snpEff</requirement> + <requirement type="package" version="1.7">SnpSift</requirement> <requirement type="set_environment">JAVA_JAR_PATH </requirement> </requirements> - <command>java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command> + <command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command> <inputs> <param format="vcf" name="input" type="data" label="VCF input"/> <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
--- a/snpSift_caseControl.xml Fri Sep 21 15:16:49 2012 -0500 +++ b/snpSift_caseControl.xml Fri Sep 21 16:00:25 2012 -0500 @@ -5,11 +5,11 @@ You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) --> <requirements> - <requirement type="package" version="3.0">snpEff</requirement> + <requirement type="package" version="1.7">SnpSift</requirement> <requirement type="set_environment">JAVA_JAR_PATH </requirement> </requirements> <command> - java -Xmx1G -jar $JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output + java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output </command> <inputs> <param format="vcf" name="input" type="data" label="VCF input"/>
--- a/snpSift_filter.xml Fri Sep 21 15:16:49 2012 -0500 +++ b/snpSift_filter.xml Fri Sep 21 16:00:25 2012 -0500 @@ -7,11 +7,11 @@ java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output --> <requirements> - <requirement type="package" version="3.0">snpEff</requirement> + <requirement type="package" version="1.7">SnpSift</requirement> <requirement type="set_environment">JAVA_JAR_PATH </requirement> </requirements> <command> - java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output + java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output </command> <inputs> <param format="vcf" name="input" type="data" label="VCF input"/>
--- a/snpSift_int.xml Fri Sep 21 15:16:49 2012 -0500 +++ b/snpSift_int.xml Fri Sep 21 16:00:25 2012 -0500 @@ -5,11 +5,11 @@ You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) --> <requirements> - <requirement type="package" version="3.0">snpEff</requirement> + <requirement type="package" version="1.7">SnpSift</requirement> <requirement type="set_environment">JAVA_JAR_PATH </requirement> </requirements> <command> - cat $input | java -Xmx2G -jar $JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output + cat $input | java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output </command> <inputs> <param format="vcf" name="input" type="data" label="VCF input"/>
--- a/tool_dependencies.xml Fri Sep 21 15:16:49 2012 -0500 +++ b/tool_dependencies.xml Fri Sep 21 16:00:25 2012 -0500 @@ -20,6 +20,15 @@ <readme> </readme> </package> + <package name="SnpSift" version="1.7"> + <install version="1.0"> + <actions> + <action type="shell_command">mkdir -p SnpSift; cd SnpSift; wget http://sourceforge.net/projects/snpeff/files/SnpSift_v1_7.jar</action> + <action type="set_environment"> + <environment_variable name="JAVA_JAR_PATH" action="prepend_to">$INSTALL_DIR/SnpSift</environment_variable> + </action> + </actions> + </install> </tool_dependency>