installing firecloud_cli error...
Hi - Having some problems installing firecloud cli: from the firecloud-cli-master area: $ sudo ./install.sh Beginning installation... Creating Python virtual environment ERROR: The executable...
View ArticleWhat actions are we allowing when we register for FireCloud?
During registration, you will be asked to Allow FireCloud to take certain actions. These actions are required for FireCloud to use Google's OAuth 2.0 protocol for authentication and authorization. By...
View ArticleString literals cannot be set to empty string
Hi Firecloud Team, When I try to run recapseg, I want to set both recapseg_workflow.recapseg_tumor_pcov.is_plotting: (String) and recapseg_workflow.recapseg_tumor_pcov.no_pon_reduction: (String) to...
View ArticleJES Error "There was a problem fetching the resource: - Rate Limit Exceeded"
Nothing seems to have failed, but the presence of the error in my log is worrying. Here's my JES log: 2016/02/04 19:34:48 I: Switching to status: start(n1-standard-1) 2016/02/04 19:37:06 I: Switching...
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Why is FireCloud requesting offline access?
When you log in to FireCloud after your account has been activated, you will be asked to allow FireCloud to have offline access. Below is an explanation of this request. Explanation FireCloud obtains...
View Article[bug] Cannot view inputs on a task
This could be related to the inputs being arrays. I have a task that merges attributes from samples in a sample_set to a single attribute on the set, and when I submit and try to click on inputs (see...
View Article[bug] If launching analysis returns 504, the analysis can still be submitted...
Hi Firecloud team, I tried to launch some analysis before on 1000 samples, and got a 504 error back. I checked the monitor tab and saw nothing new, so I assumed nothing happened. I checked my google...
View ArticleInternal Server Error Loading data Tab
Hi Firecloud Team, My data entities tab is is not loading. I only have about 600 total entities in this workspace. We tested on another laptop and got the same issue. Here's the text from the...
View ArticleFile streaming
I have broken down some of the time that is lost in running tasks in firecloud. In this example, I am running coverage collection on a single whole exome bam from the co-located tcga bucket, 12GB in...
View ArticleFirecloud UI Bug
The buttons on the method configurations tab can move when pieces of a WDL overflow their intended area (see attached photo). Under normal circumstances, the buttons stay where they are, but when I...
View Articlefirecloud error invalid choice: '\xc2\xadu' (choose from 'push', 'pull',...
Hopefully a syntax issue. Tried doing the last step in the workshop tutorial but ended up getting the following results. vpn6-54:firecloud-cli dkling$ firecloud -u...
View Articlefirecloud ui bug
When I log in after not having logged in for some days, I can see only one workspace that Eddie shared with me, "dummy". After a timeout, I relog in again, and I can see numerous other workspaces,...
View ArticleStatus "Unkown" on jobs
Hi Firecloud Team! I'm getting "Unknown" status on jobs that have completed successfully. I am running 100 jobs from a pair set of 100. Please see broad-firecloud-testing/SKCM_PanCan , submission id:...
View Article[Request] Refresh button for workflow monitor
It would be nice to have a refresh button for a particular workflow in the monitor tab rather than click the monitor tab and then select the right workflow again. This button could go right under the...
View ArticleFirecloud submits duplicate jobs within a pair_set
Hi Firecloud Team, this is about: broad-firecloud-testing/SKCM_PanCan I ran an analysis on a pair set of exactly 100 pairs. When I hit launch, it showed 100 jobs running. This is what I expected....
View ArticleAre there any public Docker images to help me build my pipeline and tools for...
If you are building a pipeline or tools to run on FireCloud, you may benefit from existing Docker images. For example, when you write the WDL for your tool, it could be easier to reference a Docker...
View ArticleHow to understand Google Cloud Project in the context of FireCloud?
Project is a central concept in the setting of Google Cloud platform. Could someone explain what roles does it play in FireCloud? How are Google projects tracked to Google billing in FireCloud? Thanks.
View ArticleFirecloud and Google Bucket API
Hi Firecloud Team! I am trying to view a pdf from a job output with PDF.JS https://mozilla.github.io/pdf.js/. In order to do this, I need to access the file. I generate a URI with...
View ArticleCloning a workspace?
At https://portal.firecloud.org/#workspaces I click on the first workspace, I come to https://portal.firecloud.org/#workspaces . I click on "+ Clone", I get the message "No Google Projects Available"....
View ArticleIs there anyone available to help with docker testing problems?
Hi Developing a module for firecloud and testing the docker for the module, I am seeing many errors from cromwell and I have no idea how to interpret the errors. Is there a docker / cromwell expert...
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