Mercurial > repos > jjohnson > snpeff_with_dep
comparison snpEff.xml @ 1:ebe280eca4a4
Add package requirement
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 13 Sep 2012 21:40:44 -0500 |
| parents | 388f178f9e13 |
| children | c641d515de2e |
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| 0:388f178f9e13 | 1:ebe280eca4a4 |
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| 4 You will need to change the path to wherever your installation is. | 4 You will need to change the path to wherever your installation is. |
| 5 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | 5 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) |
| 6 <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> | 6 <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> |
| 7 --> | 7 --> |
| 8 <requirements> | 8 <requirements> |
| 9 <requirement type="package" version="3.0f">snpEff</requirement> | |
| 9 <requirement type="set_environment">JAVA_JAR_PATH </requirement> | 10 <requirement type="set_environment">JAVA_JAR_PATH </requirement> |
| 10 </requirements> | 11 </requirements> |
| 11 <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> | 12 <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> |
| 12 <inputs> | 13 <inputs> |
| 13 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> | 14 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> |