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Possible bug in mount of .gnos #112

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SolomonShorser-OICR opened this issue Mar 2, 2016 · 0 comments
Open

Possible bug in mount of .gnos #112

SolomonShorser-OICR opened this issue Mar 2, 2016 · 0 comments
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@SolomonShorser-OICR
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See:
(develop)
https://github.com/Consonance/consonance/blob/develop/pancancer-arch-3/src/main/java/info/pancancer/arch3/worker/WorkerRunnable.java#L337
(specific commit)

consonance/pancancer-arch-3/src/main/java/info/pancancer/arch3/worker/WorkerRunnable.java

Line 337 in a262cbe

"-v", "/datastore:/datastore", "-v", "/home/" + this.userName + "/.gnos:/home/ubuntu/.gnos"));

Should probably mount to /home/seqware/.gnos instead of /home/ubuntu/.gnos since this is calling a seqware container.
SolomonShorser-OICR added a commit to ICGC-TCGA-PanCancer/OxoGWrapperWorkflow that referenced this issue Mar 2, 2016
@SolomonShorser-OICR
Consonance Worker mounts .gnos into /home/ubuntu/.gnos
ee7b62a 
...it probably should be mounted to `/home/seqware/.gnos`, but it's
easier to fix the workflow *now* to get things running, Consonance can
be fixed later. 

See this issue: 
Consonance/consonance#112
SolomonShorser-OICR added a commit to ICGC-TCGA-PanCancer/OxoGWrapperWorkflow that referenced this issue Mar 3, 2016
@SolomonShorser-OICR
Consonance Worker mounts to /home/ubuntu/.gnos/
177281b 
See: Consonance/consonance#112
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@SolomonShorser-OICR