Arvados

03/01/2019

03:18 PM Arvados Support #14906: [SDK] Maintain Arvados SDKs in Bioconda

This would be great and happy to help. You've already got the relevant recipes listed above. Bioconda is an open proj... Brad Chapman

02/24/2019

10:46 AM Arvados Revision a1aefe79 (arvados): Python 3: move to recent ciso8601 2.x branch

Older ciso8601 versions are not built for Python 3.7 which
prevents migration to latest Python on conda packaging. Th... Brad Chapman

02/15/2019

03:54 PM Arvados Revision 13fa7686 (arvados): Python 3: only import subprocess32 on py27

Avoids the need to install and import subprocess32 when working
with any recent Python 3.x version. This helps with b... Brad Chapman

11/27/2017

02:53 AM Arvados Idea #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... Brad Chapman

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... Brad Chapman

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:... Brad Chapman

02:46 PM Arvados Bug #12606 (Resolved): 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... Brad Chapman

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... Brad Chapman

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... Brad Chapman

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... Brad Chapman