adamnovak on 4094-fix-s3-cwl
Fix HTTP downloads and colons i… (compare)
adamnovak on 4094-fix-s3-cwl
Report what can't be copied ser… Add tests for Directory import … (compare)
adamnovak on 4094-fix-s3-cwl
Note when AWS won't allow you t… (compare)
w-gao on 4079-suppress-pytest-warnings
Register pytest markers Merge branch 'master' into issu… (compare)
adamnovak on 3917-toil-kill-on-different-machine-from-leader
Mention --export=ALL for SLURM … Merge branch 'master' into issu… (compare)
adamnovak on 4094-fix-s3-cwl
Try to actually talk to out-of-… (compare)
adamnovak on 4094-fix-s3-cwl
Mention --export=ALL for SLURM … Merge remote-tracking branch 'u… Handle file paths as well as fi… (compare)
mr-c on master
Mention --export=ALL for SLURM … (compare)
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
[Adam Novak, UCSC GI] @cibinsb, if you are setting up your own AWS roles/credentials (instead of using toil launch-cluster
), you need to make sure you are granting access to SimpleDB in addition to access to S3, for the AWS job store to work.
As described in https://toil.readthedocs.io/en/latest/running/cloud/kubernetes.html#aws-job-store-for-kubernetes you need to grab some AWS credentials, put them in a Kubernetes secret, and use TOIL_AWS_SECRET_NAME
when you run the workflow, to grant the workers access. You also need to make sure the leader has access, either by running it in a pod with the secret mounted in to ~/.aws
, or by setting up ~/.aws
on whatever non-pod machine you are running the leader on.
toil-test--files
? That sounds like a very generic name, and bucket names must be unique across all of AWS. It is quite possible that someone else is already using the jobstore named toil-test
and that you will have to pick a different, unique name.