Mercurial > repos > greg > snpeff_v2_from_pablo
comparison snpEff_2_1a/scripts/snpSift.sh @ 0:f8eaa3f8194b default tip
Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
| author | greg |
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| date | Fri, 20 Apr 2012 14:47:09 -0400 |
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| -1:000000000000 | 0:f8eaa3f8194b |
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| 1 #!/bin/sh | |
| 2 | |
| 3 DIR=$HOME/snpEff/ | |
| 4 DIR_SNPSIFT=$HOME/snpEff/snpSiftBin/ | |
| 5 LIB=$HOME/snpEff/lib | |
| 6 LIB_SNPSIFT=$HOME/snpEff/snpSiftLib/ | |
| 7 | |
| 8 # Old library reference: | |
| 9 # -classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR:$DIR_SNPSIFT" \ | |
| 10 | |
| 11 java -Xmx1G \ | |
| 12 -classpath "$LIB/charts4j-1.2.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$LIB_SNPSIFT/antlr-3.4-complete.jar:$DIR:$DIR_SNPSIFT" \ | |
| 13 ca.mcgill.mcb.pcingola.vcfEtc.SnpSift \ | |
| 14 $* | |
| 15 |