Mercurial > repos > greg > snpeff_v2_from_pablo
diff snpEff_2_1a/scripts/snpSift.sh @ 0:f8eaa3f8194b default tip
Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
| author | greg |
|---|---|
| date | Fri, 20 Apr 2012 14:47:09 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/snpSift.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,15 @@ +#!/bin/sh + +DIR=$HOME/snpEff/ +DIR_SNPSIFT=$HOME/snpEff/snpSiftBin/ +LIB=$HOME/snpEff/lib +LIB_SNPSIFT=$HOME/snpEff/snpSiftLib/ + +# Old library reference: +# -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:$DIR_SNPSIFT" \ + +java -Xmx1G \ + -classpath "$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" \ + ca.mcgill.mcb.pcingola.vcfEtc.SnpSift \ + $* +