Email for quota increase requests
Hi, We want to submit a request to increase a quota for one of our workspaces. However, it appears help@firecloud.org is no longer being used for FC support. What is the current mechanism for...
View ArticleComments on FireCloud DataShuttle
I installed the client, and then tried to log in. It said I could use my google login, which I presume meant that Google single-signin would work, but the app then proceeded to ask me for my google...
View ArticleClik here to view.
Workflow "Running" but call stuck at "QueuedInCromwell"
Hi, When submitting a job to the pici-firecloud/Pre-processing_b37_v3 workflow, the workflow doesn't seem to be starting even though the status is listed as running, and has been stuck at this status...
View ArticleNotebooks - docker images
It would be a nice feature if I could specify a docker image to use when I start a Jupyter notebook. This would make it easier for to reproduce your analyses. Thanks.
View ArticleJobs say `Requesting Execution Token` since last night
Sometime yesterday afternoon all of my submissions started showing up as Requesting Execution Token for 6+ hours. This morning they haven't moved so I'm aborting them and restarting them. So far the...
View ArticleNotebook: R kernel, exporting/downloading notebooks
From an R notebook, this is what I see when I try to export the Notebooks to PDF: nbconvert failed: xelatex not found on PATH, if you have not installed xelatex you may need to do so. Find further...
View ArticleClik here to view.
QueuedInCromwell
Tacking on another thread to further highlight Had a job stuck for 8 hours last night
View ArticleCost associated with workflow
The May 17th release notes write, Actual workflow run cost is now returned in the submission status API, when available. This will be available in the UI soon. I am observing that workflows run today...
View ArticleData access
Hi, FireCloud Team, We are part of the MESA TOPMed Transomics Pilot Study. We are working with MESA to obtain permission for using the TOPMed WGS BAM files, which we understand reside at the Broad....
View ArticlePossible to add a column to Sample Set data table?
I'm running a method that uses Sample Set as the root entity. For this method, I'm using a file that is different depending on the sample set that's being run. I'd like to be able to specify something...
View ArticleClik here to view.
Clik here to view.
Downloading Participant Metadata
When you right click on Download Participant Metadata you get the following menu: It would be great to have a Copy Link Address option in that menu. This would help me download it on the command line...
View ArticleClik here to view.
Notes column in Monitor tab
These are the current columns on the Monitor tab: I'd love to have an additional column called Notes or something like that, that I could add text to from Firecloud. Sometimes I like to make a note to...
View ArticleClik here to view.
API and workspaces unresponsive
I'm getting errors with the API and when trying to access workspaces through the UI.
View Articlerawls time-out error on submission
I'm getting the same error on almost all of my submissions: "messages":["ErrorReport(rawls,http call failed: https://cromwell1-int-lb.dsde-prod.broadinstitute.org:443/api/workflows/v1/batch: TCP...
View ArticleClik here to view.
Subworkflow links to wrong bucket location
I've been using the subworkflow information that got added recently (thank you so much!) on the monitor page. When you click on a task link in a subworkflow it takes you to a nonexistent bucket...
View ArticleIssue related upload data to Firecloud bucket from another Google cloud bucket
Hi, I have data stored in google cloud bucket gs://PROJECT_A and i want to upload those data to firecloud to run GATK pipeline. Both project A google bucket and FireCloud workspace have the same Broad...
View ArticleUnable to access Firecloud account
Hi, I had registered for Firecloud a while back, however, recently, I am unable to access it through https://portal.firecloud.org. When I click on sign-in it and select my broad account it does...
View ArticleUploading data to FireCloud bucket from Google Compute Engine in another...
I have been working on a VM in a google project called "PROJECT1" (for example) and I have data on that VM that I want to transfer to FireCloud. My FireCloud workspace is under a different google...
View ArticleA tool works on a sample but not when I run it on a sample pair.
Is there a problem with the FIRECLOUD system? Thanks, Yosi
View Article