Mercurial > repos > jjohnson > snpeff_with_dep
comparison snpEff_download.xml @ 14:ef4598ea7179
Add SnpSift dependency
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 21 Sep 2012 16:00:25 -0500 |
| parents | e9e4ff80e72b |
| children | aab5e0adb26d |
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| 13:d57983929080 | 14:ef4598ea7179 |
|---|---|
| 2 <description>Download a new database</description> | 2 <description>Download a new database</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="3.0">snpEff</requirement> | 4 <requirement type="package" version="3.0">snpEff</requirement> |
| 5 <requirement type="set_environment">JAVA_JAR_PATH </requirement> | 5 <requirement type="set_environment">JAVA_JAR_PATH </requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <command>java -jar $JAVA_JAR_PATH/snpEff.jar download -c $JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> | 7 <command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> |
| 8 <inputs> | 8 <inputs> |
| 9 <param name="genomeVersion" type="select" label="Genome"> | 9 <param name="genomeVersion" type="select" label="Genome"> |
| 10 <option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option> | 10 <option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option> |
| 11 <option value="ailMel1.66">Ailuropoda melanoleuca : ailMel1.66</option> | 11 <option value="ailMel1.66">Ailuropoda melanoleuca : ailMel1.66</option> |
| 12 <option value="ailMel1.65">Ailuropoda melanoleuca : ailMel1.65</option> | 12 <option value="ailMel1.65">Ailuropoda melanoleuca : ailMel1.65</option> |