cromshell
cromshell copied to clipboard
broadinstitute
CLI for interacting with Cromwell servers
Sometimes: 1. I abort a job by their ID 1. when I run "cromshell list" I see that the job is listed as still running. 2. if I try to...
It would be very convenient if cromshell zipped up a given directory of wdl files for you rather than requiring you to always supply a pre-zipped file.
Hi there, I cannot figure out how to run cromshell from an hpc - I have changed the url for any open ports and it still says 'cannot communicate with...
@yfarjoun pointed out that a lot of the operations we do for cromshell have firecloud equivalents. Moreover, firecloud also has a nice [swagger API](api.firecloud.org). I think we should add in...
Ultimately, this seems like—at minimum a confusing naming scheme—a "feature" from cromwell. So, I accidentally noticed some big discrepancies between timestamps in task backend logs and timestamps in cromwell metadata....
> cromshell list -u -c reports that job_id: 607c742d-9327-49b4-a621-d2a28aa48f17 is running However: > cromshell status 607c742d-9327-49b4-a621-d2a28aa48f17 reports that the job is aborted. The latter is consistent with what is reported...
I'm running into a possible edge case where the gather step in a 3000 scatter-gather pipeline takes more than 90 minutes to get started. Shouldn't be hard to implement, just...
abort leaves some curl output on the terminal ``` "" "" "" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed...
There are multiple failure modes when the server times out and they report differently but without a clear indication why. ``` 🐳 local_alleles 1.8 cromshell metadata > meta Sub-Command: metadata...