Stephanie Gogarten

1. Community
2. Active Feature Requests
3. Private WDL Github Sync

This feature would also be very useful for testing workflows before they're ready to be shared with others. I'd prefer if my public Dockstore workflows were not cluttered with things like "test dat...

• View comment
• January 05, 2022 00:23
• 2 votes

1. Community
2. Completed Feature Requests
3. Remove a workspace from "My Workspaces"?

I see that this feature has been implemented, but it seems limited to workspaces that have been shared with me directly, and I can't use it for the workspaces I would most like to remove from my li...

• View comment
• Edited December 16, 2022 22:41
• 1 vote

1. Community
2. Active Feature Requests
3. RStudio and Jupyter in one environment

I especially want to upvote the request to have RStudio notebooks viewable under the "Notebooks" tab. Many researchers prefer working in RStudio, and being able to quickly view the .nb.html output ...

• View comment
• March 31, 2022 19:30
• 1 vote

1. Community
2. General Discussion
3. tnu drs commands returning error code

I submitted a separate ticket about the error in relinking accounts; it was a bug and has now been fixed. The issue above seems to have resolved as well; `tnu drs info` gives the expected response.

• View comment
• April 18, 2024 16:36
• 0 votes

1. Community
2. General Discussion
3. How to index a CRAM file on Terra with samtools?

Thanks Ash! I feel like the bigger issue here is a failure of Dockstore search, because even knowing that the exact workflow I want exists, it's not straightforward to find it. I posted about this ...

• View comment
• Edited August 30, 2023 22:09
• 0 votes

1. Community
2. General Discussion
3. How to index a CRAM file on Terra with samtools?

Is there now a readily available WDL to run `samtools index`? I tried searching for one on dockstore, but got >200 results for WDLs that contain indexing somewhere as a step. I also tried searching...

• View comment
• August 29, 2023 23:00
• 0 votes

1. Community
2. Completed Feature Requests
3. Set metadata column order during tsv upload

Is it possible to preserve the ordering in the initial TSV file (or Python/R table when interacting with data tables programmatically)? Our project will be creating hundreds of workspaces, so chang...

• View comment
• February 10, 2023 23:18
• 0 votes

1. Community
2. General Discussion
3. Error "Permission 'storage.buckets.list' denied on resource" when using gsutil

Interesting, when I click on the file (which has a DRS identifier), I get a curl command to download instead of gsutil. So maybe this is a known limitation of gsutil for controlled access data; it ...

• View comment
• February 01, 2023 19:40
• 0 votes

1. Community
2. General Discussion
3. Error "Permission 'storage.buckets.list' denied on resource" when using gsutil

I just tried again after several days and got the same error: gsutil -u terra-c9b4d853 cp gs://nih-nhlbi-topmed-released-phs000964-c3/phs000964.v3.pht004839.v2.p1.TOPMed_WGS_JHS_Sample.MULTI.txt.gz...

• View comment
• January 31, 2023 21:33
• 0 votes

1. Community
2. General Discussion
3. Error "Permission 'storage.buckets.list' denied on resource" when using gsutil

I have linked my NIH account, as well as my account with NHLBI BioData Catalyst Framework Services, which is what gives me access to this particular file via its DRS and terra-notebook-utils. I jus...

• View comment
• January 26, 2023 17:37
• 0 votes