Mercurial > repos > jjohnson > snpeff_with_dep
comparison snpSift_annotate.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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| 3 <!-- | 3 <!-- |
| 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, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | 5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) |
| 6 --> | 6 --> |
| 7 <requirements> | 7 <requirements> |
| 8 <requirement type="package" version="3.0f">snpEff</requirement> | |
| 8 <requirement type="set_environment">JAVA_JAR_PATH </requirement> | 9 <requirement type="set_environment">JAVA_JAR_PATH </requirement> |
| 9 </requirements> | 10 </requirements> |
| 10 <command>java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command> | 11 <command>java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command> |
| 11 <inputs> | 12 <inputs> |
| 12 <param format="vcf" name="input" type="data" label="VCF input"/> | 13 <param format="vcf" name="input" type="data" label="VCF input"/> |