Quantcast
Channel: Ask the FireCloud Team — GATK-Forum
Browsing all 1147 articles
Browse latest View live

Docker best practices

Is there a prefered base image to use for Docker images on FireCloud? Internally, I've seen a lot of use of ubuntu:16.04, but looking at some of the language-based official docker images on dockerhub...

View Article


broken links to workspaces in documentation ?

Links to workspaces are broken in the documentation. To see examples: 1) go here : https://software.broadinstitute.org/firecloud/documentation/ 2) click on "Getting Started" 3) then "FireCloud Basics"...

View Article


Are config namespaces helpful/necessary within workspaces?

Hi Team, Over the last couple of days I've had the recurring thought that it's over-engineering to require config namespaces in workspaces. I can understand how for the Method repository such scoping...

View Article

In the method repository, what does a type of "Task" mean?

Within the method repository I understand the types of "Configuration" and "Workflow" and these seem to be the overwhelmingly significant instances of methods in the repository. But there is a third...

View Article

"Workflow ID" link to google bucket for a workflow stopped working

Hi, Today when clicking on the "Workflow ID" link from the workflow page, expecting to see workflow stuff in a google bucket, it switches google accounts from stewart@broadinstitute.org (logged into...

View Article


Failure to delocalize file, and failures due to invalid google credentials

In my recent firecloud runs I've had a few jobs fail. The following two errors have happened multiple times, but I give just one example of each. Are there any suggestions for dealing with each of...

View Article

RFE: utilize the parameter_meta section of WDL in the Method Configuration UI

It would be really nice if the Method Configuration UI in-lined parameter descriptions with their associated parameters when the WDL has a parameter_meta section, especially in tasks that have lots of...

View Article

Groups API calls not linked to web interface functionality?

Hi, I've been trying to use the newly released feature below from the release notes here - https://software.broadinstitute.org/firecloud/blog?id=9364: You can now use the FireCloud APIs to create and...

View Article


What are the restrictions for attribute names?

Are there any naming conventions (i.e., technical restrictions) on the names that are used for entity attributes and workspace attributes? thanks!

View Article


Image may be NSFW.
Clik here to view.

File Details for Zip files displays gibberish in preview

When I look at a zip file attached to a sample set annotation, I get the following: A better preview would be a content listing, or nothing at all.

View Article

something went wrong

I click among the tabs of a workspace (summary, Data, method configurations....) perhaps "too fast" for firecloud and I see the attached error. I saw it twice by just clicking around the tabs...

View Article

Using the GUI I can't edit the auth domains I created earlier using the API

About a month or more ago I created two Authorization Domains: BroadIBM_Resistance Getz_Lab_Test When I go to the groups panel (through the groups menu selection under my name), it says I am a member...

View Article

group name for TCGA Controlled Access Authorization Domain should be changed.

Currently the group name for the TCGA Controlled Access Authorization Domain is dbGapAuthorizedUsers. Once we get support for the TARGET Authorization domain in place, we are probably going to want to...

View Article


Image may be NSFW.
Clik here to view.

Attribute column order in Data view is not lexicographical

See the sample_set tab here: https://portal.firecloud.org/#workspaces/broad-firecloud-gdac/dev/data Or simply looking at the filter modal: There does not appear to be a consistent ordering to the...

View Article

RFE: Include attribute column names in search in Workspace Data tab

Since attributes can pile up over time, having a way to filter them based on nomenclature would be extremely useful. E.g.: I have multiple attributes on a sample_set entity that end in __pkg, and I...

View Article


Something went wrong ... after uploading workspace attributes

I cloned a workspace, then downloaded the attributes (by clicking "Download Attributes") then, without editing the TSV I upload right back the TSV and I see the "something went wrong" (see attached). I...

View Article

Image may be NSFW.
Clik here to view.

Minor display bug: Import Data button squishes weirdly a participant ID is...

Clicking a participant ID brings up more data on the right side of the screen, which causes the control panel on top to be weirdly squished and the ImportData button to become two lines high. See the...

View Article


timeline for upgrading to Cromwell27 (from current 26?)

Does anybody by chance know the timeline for upgrading FC cromwell 26 to 27? -eddie

View Article

tasks run forever with incorrect GS-URLS....an error should arise instead

See the WDL here and attached screenshot. task catter_task { File myFile command <<< #increase verbosity set -x #show the file contents cat ${myFile} >>> runtime { docker :...

View Article

Wrong path to file after executing method to index a BAM in another google...

Hello -- We created a very simple WDL which indexes a BAM file. The BAM is located in another google bucket, and the index file is created within the Workspace google bucket. But the resulting path to...

View Article
Browsing all 1147 articles
Browse latest View live