Mercurial > repos > jjohnson > snpeff_with_dep
comparison snpSift_annotate.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 |
|---|---|
| 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="1.7">SnpSift</requirement> | 8 <requirement type="package" version="1.7">SnpSift</requirement> |
| 9 <requirement type="set_environment">JAVA_JAR_PATH </requirement> | |
| 10 </requirements> | 9 </requirements> |
| 11 <command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command> | 10 <command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command> |
| 12 <inputs> | 11 <inputs> |
| 13 <param format="vcf" name="input" type="data" label="VCF input"/> | 12 <param format="vcf" name="input" type="data" label="VCF input"/> |
| 14 <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."/> | 13 <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."/> |