Mercurial > repos > jjohnson > snpeff_with_dep
comparison snpEff.xml @ 17:aab5e0adb26d
Remove environment requirement
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 21 Sep 2012 18:23:28 -0500 |
| parents | ef4598ea7179 |
| children | 1cae7fb31da7 |
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| 16:24c77a318a0f | 17:aab5e0adb26d |
|---|---|
| 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="3.0">snpEff</requirement> | 9 <requirement type="package" version="3.0">snpEff</requirement> |
| 10 <requirement type="set_environment">JAVA_JAR_PATH </requirement> | |
| 11 </requirements> | 10 </requirements> |
| 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> | 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> |
| 13 <inputs> | 12 <inputs> |
| 14 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> | 13 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> |
| 15 | 14 |