Scott Ouellette
Scott Ouellette
~~~FWIW An identical run outside of Galaxy & SLURM still yields a segfault~~~ EDIT: 8-24-18 I haven't been able to reproduce the segfault outside of SLURM
@rob-p Thanks for your quick reply! I'll try this out with a more recent conda installation of salmon and report back
I've created a new conda environment based off of `salmon==0.11.2` and was able to run it successfully outside of Galaxy/SLURM on the same 14.04 instance. I had to omit the...
@rob-p I've taken the time to [update salmon to 0.11.2 in it's respective Galaxy Tool wrapper](https://github.com/bgruening/galaxytools/pull/778) and am still seeing the `salmon quant` segfault when running through SLURM. bioconda installs...
@bgruening Almost. The same command copy and pasted from the failed Galaxy job works outside of SLURM on the same worker node. I haven't tried submitting to SLURM from outside...
@bgruening So I've tried some runs today with higher memory configurations and can still reproduce the segfault. I'm going to continue on and try to write up a reproducer for...
@dpryan79 Thanks for trying to reproduce, I really appreciate this. We're currently bringing up CloudMan instances derived from shared cluster strings. I'll try to bring up a fresh CloudMan instance...
@nsheff Sorry I was never able to dig into this further
Django Upgrade
I'd prefer option C to keep some uniformity as to how we are adding these files, while still providing a convenience with less clicks for the user. It would also...