Mercurial > repos > jjohnson > snpeff_with_dep
comparison snpEff_download.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 |
comparison
equal
deleted
inserted
replaced
| 16:24c77a318a0f | 17:aab5e0adb26d |
|---|---|
| 1 <tool id="snpEff_download" name="SnpEff Download" version="1.0"> | 1 <tool id="snpEff_download" name="SnpEff Download" version="1.0"> |
| 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> | |
| 6 </requirements> | 5 </requirements> |
| 7 <command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> | 6 <command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> |
| 8 <inputs> | 7 <inputs> |
| 9 <param name="genomeVersion" type="select" label="Genome"> | 8 <param name="genomeVersion" type="select" label="Genome"> |
| 10 <option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option> | 9 <option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option> |