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genome / gms

The Genome Modeling System installer
https://github.com/genome/gms/wiki
GNU Lesser General Public License v3.0
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bam-readcount fails due to hard coding to VarScan.v2.2.9.jar #102

Closed malachig closed 10 years ago

malachig commented 10 years ago

Calls to gmt analysis coverage bam-readcount fail because this module has this hard coding in it:

my $cmd = "java -jar /gsc/scripts/lib/java/VarScan/VarScan.v2.2.9.jar readcounts $tempdir/pileup --min-coverage 1 --min-base-qual $min_base_quality --output-file $tempdir/indels.varscan";

It appears that this is has already been fixed in master and therefore should in theory be resolved if we merge master into gms-pub again...

malachig commented 10 years ago

It looks like the latest round of merging has resolved this issue. bam-readcount commands now succeed without error. Closing this issue.