Brad Chapman

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11/27/2017

02:53 AM Arvados Story #12666 (New): --ignore-docker-for-reuse not passed to crunch v2 jobs started via --submit --no-wait
I often make use of `--ignore-docker-for-reuse` during bcbio runs since I'll fix bugs, re-create and re-upload the bc...

11/17/2017

07:09 PM Arvados Bug #12606: Symlink in output points to invalid location -- no such file or directory
Thanks Peter. I'll work around this by avoiding the symlinks and copying the files out of the strelka2 specific direc...
02:48 PM Arvados Bug #12606: Symlink in output points to invalid location -- no such file or directory
Sorry the error message got formatted all on one line for some reason. Here it is in a more readable format:...
02:46 PM Arvados Bug #12606 (New): Symlink in output points to invalid location -- no such file or directory
Hi all;
I'm running into an issue on runs with symlinked outputs, specifically for strelka2 variant calling. The run...

11/16/2017

02:09 PM Arvados Bug #12593 (Closed): Unable to resolve localhost in GATK4 log4j setup
Nico and Tom -- thanks again for the help. The `arv:APIRequirement` trick seems to have done it and I can now progres...

11/14/2017

06:51 PM Arvados Bug #12593: Unable to resolve localhost in GATK4 log4j setup
Sorry I shouldn't read this in a meeting: `arv:APIRequirement` to the `requirements`. Got it. I'll give that a try an...
06:48 PM Arvados Bug #12593: Unable to resolve localhost in GATK4 log4j setup
Nico and Tom -- thanks so much for digging into this. This is really helpful. log4j bundled with the GATK jar so I do...

11/11/2017

11:08 AM Arvados Bug #12593 (Closed): Unable to resolve localhost in GATK4 log4j setup
I'm running into an issue running bcbio workflows with GATK4, where they fail in a localhost lookup when setting up l...

04/14/2017

12:27 AM Arvados Bug #11495: bcbio NA12878 validation runs: job re-use failure with non-existant collection
Thanks Bryan for the digging on this. I didn't intentionally delete any log files but am not sure if the failed retri...

04/13/2017

01:46 PM Arvados Bug #11495 (New): bcbio NA12878 validation runs: job re-use failure with non-existant collection
Due to failures reported in #11494 I tried to re-run the bcbio CWL validation pipeline with re-use enabled and I get ...

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