Nate Coraor
Nate Coraor
This adds 7 new job and dataset states: - **waiting**: The dataset has been picked up by a handler (only used by the `db-skip-locked` and `db-transaction-isolation` handler assignment methods) but...
In order to support this, I've added a new metric type, the "file" metric. The reasoning is that this is probably going to be too much data to put in...
Rather than fix every tool that writes to its inputs directory, we can just symlink inputs to a subdir of the job directory. Bonus features: - Inputs are symlinked with...
An issue for collecting things we notice during the 2020 Galaxy Admin Training in Barcelona that need to be fixed - [x] Decide how to handle variables (set custom vs...
Binary objects built on a CPython that's built with Pydebug (`--with-pydebug`) are incompatible with objects built on non-pydebug CPythons (this is the `d` in PEP 425 tags). The software I...
And probably tmpwatch/tmpreaper for the scratch and jobs directories
I was digging a bit to find out if the `rna_star` assets were built with STAR 2.7.x since I believe they're not compatible with older versions, and that raised a...
Systemd expects the process it execs to continue running and stay foregrounded, which is incompatible with the way that SIGUSR2 zero-downtime reloading works. This is because after sending the final...
Add the container monitor script to the galaxy-job-execution package so that it can be installed standalone. This is useful if you are running GxITs via Pulsar. First implemented in #9349...
From Gitter: @natefoo > It looks like Trinity with the genome-guided option selected produces outputs with -GG in the filename but the wrapper doesn't account for this? From the Trinity...