Hexotical on 3514-missing-permission-warning-aws
Performance testing for Gravito… Issues/2501 file store case ins… cache results of cwltool versio… and 7 more (compare)
Hexotical on 3514-missing-permission-warning-aws
Fix iam.py to pass tests (compare)
Hexotical on 3514-missing-permission-warning-aws
Type iam.py to pass mypy check (compare)
Hexotical on 3514-missing-permission-warning-aws
Remove unused import in aws pro… (compare)
Hexotical on 3514-missing-permission-warning-aws
Address PR comments, remove uti… (compare)
mr-c on 3131-do-not-submit-empty-jobs
Update leader.py (compare)
file_store.readGlobalFileStream
so any inputs regarding that would be much appreciated
Okay, thank you for the feedback!
I've made some changes - if it looks good, may I go ahead and submit the proposal?
FileNotFoundError: [Errno 2] No such file or directory: '_:file:///juno/work/access/testing/users/johnsoni/access_qc/work5/f26b1779cb2f5ea39419d80a2066faf9/e81b/360a/tmpb4cbwihh/out/simplex_bam_pool_a_dir'
toilfs:16305:0:files/for-job/kind-CWLJob/instance-7ousmklr/file-184521b84be2407b8ea6ef01398c6f81/histogram.pdf
[Adam Novak, UCSC GI] @ionox0 This is part of the not-actually-correct logic that Toil has for preparing directories for CWL workflows. The underscore prefix is something that cwltool
uses that indicates a directory is to be created to present to a CWL tool. Toil tries to generate this to control cwltool
, but in practice what we have in 5.4 only works when running on a single machine or otherwise using a shared filesystem between nodes.
I've been redoing all that logic in DataBiosphere/toil#3628 so that Toil can be responsible for setting up the directory structures that CWL tools expect to see, whether there's a shared filesystem or not, but I still don't have it fully working yet. When it's done, it should be much harder to break.
exit code 120
pointing to ?
SoftwareRequirement
handling)
Hi all,
I'm trying to run toil on the internal Kubernetes cluster, following is the command which I used
toil-cwl-runner --logDebug --enable-dev --batchSystem kubernetes --jobStore aws:us-east-1:toil-test --stats --singularity --defaultCores 1 md_launch.cwl md_list_input_descriptions.yml
but I'm getting a permission error
<Response><Errors><Error><Code>AuthorizationFailure</Code><Message>User (arn:aws:iam::07445xxxxxx:user/cibin) does not have permission to perform (sdb:Select) on resource (arn:aws:sdb:us-east-1:074455289529:domain/toil-registry). Contact account owner.</Message><BoxUsage>0.0000137200</BoxUsage></Error></Errors><RequestID>0e71b5c9-150a-b570-a5cf-31f1f751abca</RequestID></Response>
Toil version is 5.4.0