How to statistics with the TCGA data available on FireCloud?
Hi! I want to do statistics with the TCGA data available on FireCloud, especially the number of patients with RNA-seq bam files (or WXS bam files) of each cancer. Would you please to guide me how to...
View ArticleQuery about update of TCGA data on FireCloud
Hi! I know that TCGA data have moved to GDC. I wonder that if the TCGA data on FireCloud have updated recently or not? If Not, when will FireCloud update the TCGA data. Our team wants to use FireCloud...
View ArticleUI for creating methods?
Hi - I'm trying to create a new, very simple task (just 'hello world', really), and have read the Tool Developer Basics gdoc. However, I couldn't help but notice that there's also a big "Create New...
View ArticleFireCloud jobs Exception: workflows failed
My workflows running on FireCloud all failed since yesterday (2016-11-14). I have run hundreds of jobs on FireCloud successfully before. Would you please to check out what happen? Thank you very much....
View ArticleCannot download results from FireCloud using gsutil
Hi, FireCloud team. I found that I cannot download results from FireCloud using gsutil since yesterday (11/21/2016). The error message is the following: Unable to find the server at www.googleapis.com...
View ArticleData table only shows attributes if at least one entity on the first page has...
1) Create a new workspace 2) Upload the following participants loadfile (also attached): entity:participant_id attr1 attr2 01 value01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 value21...
View ArticleUpdating data model and method configuration outputs do not appear in data...
I'm having problems updating the data model in a workspace. Specifically, I'm trying to update Sample attributes (add columns to the data model) through (1) an "update:sample_id" tsv file, which...
View Articlecan't launch workflow
I try to launch some test workflow and everytime I get mistake "POST request to /api/workflows/v1/batch timed out". I found that this mistake can be related with cromwell's inner work, but may be I do...
View Article500 Errors submitting membership TSV file
I am trying to submit a large membership tsv file (63K lines), and I've written a FISSFC command (available in v0.13.1) to batch the update into multiple smaller groups (default is 500, but...
View ArticleMethod configuration to access sample attribute values in sample set
I am configuring a method for a sample set. In my data model, my samples have an attribute called clean_results_file, and I would like to access these attribute values for all samples in a sample set....
View ArticleUnable to access gs://firecloud-tcga-open-access/tutorial
Attempted to follow tutorial here: http://gatkforums.broadinstitute.org/firecloud/discussion/6863/broad-mini-mutation-calling-workflow After creating a billing enabled project and cloning the...
View ArticleGetting many "Error! See details below." messages when trying to view files
Most files that I try to view result in a message: Error! See details below. { "statusCode": 500, "source": "FireCloud", "timestamp": 1482381089293, "causes": [{ "source": "FireCloud", "message": "key...
View Articlesubmitted status in during long time
I launched the workflow around 2 hours ago and it still has a status "submitted". When I try to launch any different workflow I have a same problem, they don't work and has submitted status....
View ArticleDuplicate Samples in same Sample Set
Hi Firecloud, When importing samples to a sample set which already exist in that sample set, firecloud duplicates the samples without throwing an error or saying anything. So, after importing samples...
View ArticleProject i-dotting and t-crossing
Dear FireCloud Team, I am co-investigator on the broad-firecloud-cptac billing project but am only listed as "user" not "Owner". Please make me "Owner," so that at my discretion I may add others later....
View ArticleCan you provide a detailed explanation of workflow timing diagram?
Looking at the workflow diagram, I see for each call a multi-colored bar describing the changing state of a job (called task) on FireCloud. The GUI makes it difficult to get information on each of the...
View ArticleMoved: Can you provide a detailed explanation of workflow timing diagram?
This discussion has been moved.
View Article