Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Created FuncotatorDataSourceBundler Tool #7427

Open
wants to merge 49 commits into
base: master
Choose a base branch
from

Conversation

haileypfox
Copy link
Contributor

No description provided.

@gatk-bot
Copy link

gatk-bot commented Aug 19, 2021

Travis reported job failures from build 35614
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 35614.13 logs
integration openjdk11 35614.12 logs
unit openjdk8 35614.3 logs
integration openjdk8 35614.2 logs

@jonn-smith jonn-smith marked this pull request as draft September 1, 2021 21:52
@gatk-bot
Copy link

gatk-bot commented Sep 1, 2021

Travis reported job failures from build 35833
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 35833.13 logs
integration openjdk11 35833.12 logs
unit openjdk8 35833.3 logs
integration openjdk8 35833.2 logs

@gatk-bot
Copy link

gatk-bot commented Nov 16, 2021

Travis reported job failures from build 36902
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 36902.13 logs
unit openjdk8 36902.3 logs

@gatk-bot
Copy link

gatk-bot commented Nov 16, 2021

Travis reported job failures from build 36904
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 36904.13 logs
unit openjdk8 36904.3 logs

@gatk-bot
Copy link

Travis reported job failures from build 36908
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud openjdk11 36908.14 logs

@gatk-bot
Copy link

gatk-bot commented Nov 16, 2021

Travis reported job failures from build 36910
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 36910.13 logs
unit openjdk8 36910.3 logs

@jonn-smith jonn-smith marked this pull request as ready for review November 17, 2021 00:41
@jonn-smith
Copy link
Collaborator

@droazen OK - I think it's ready for your review.

Copy link
Contributor

@droazen droazen left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@jonn-smith Back to you with my comments. Please go ahead and merge after addressing them.

@droazen droazen removed their assignment Nov 19, 2021
@gatk-bot
Copy link

gatk-bot commented Nov 23, 2021

Travis reported job failures from build 36989
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 36989.13 logs
unit openjdk8 36989.3 logs

- Bumped the version of Ensembl used by the downloader tool to 52.
- Added a test to regenerate the expected output for
  `testDownloadDatasourcesWithValidation`.
- Updated expected results for `testDownloadDatasourcesWithValidation`.
@robby81
Copy link

robby81 commented May 24, 2022

Is there still anything missing? It is not merged since quite some time. The funcotator data sources in version 1.7 are already lacking at least 2 years behind the current databases. I would like to see a possibility to create own and updated bundles merged.
Thanks!

@droazen
Copy link
Contributor

droazen commented May 24, 2022

@robby81 There are still one or two issues with the tool that need to be resolved before this can be merged, unfortunately. @jonn-smith will be resuming work on these shortly -- we do want to get this tool into GATK soon to make it easier to create custom Funcotator datasources!

@robby81
Copy link

robby81 commented Aug 30, 2022

@droazen We are still on hold for update the Funcotator datasources. Especially getting new versions of gencode would be desirable and does not work with the current scripts. We already started looking for alternatives for our routine diagnostics workflow.

@jonn-smith
Copy link
Collaborator

@robby81 Which scripts are you running and what are the errors you see? The data sources scripts are unsupported, but should work out of the box (they did last time I tried them).

@robby81
Copy link

robby81 commented Aug 30, 2022 via email

@jonn-smith
Copy link
Collaborator

@robby81 Ah, OK. Yeah - this is a problem in the parser I wrote. I was trying to be very specific about what was allowed so users could not build erroneous data sources.

This is high on my list of fixes. I'm trying to get some time to do them.

@robby81
Copy link

robby81 commented Oct 11, 2022 via email

@robby81
Copy link

robby81 commented Apr 5, 2023

Whats the status here? Also the bundled sources got no updates since 2020.

@jonn-smith
Copy link
Collaborator

@robby81 This still has to be merged. I've been pulled off onto some other projects for a bit. Some changes to the internals of Funcotator are needed for this tool to be most useful, so I was waiting until those updates were made to merge this.

I can compile a new release of the data sources, but I haven't heard from anyone in the community that it's a priority. Can you create a new issue for it? Some questions around a new release: If I were to create one, what would the new release include? Would there be any new data sources that were not included before? Are any included data sources no longer useful and should be removed?

@dheiman
Copy link

dheiman commented Apr 5, 2023 via email

@robby81
Copy link

robby81 commented Jul 27, 2023

Is there anything happening on this front?

@jonn-smith
Copy link
Collaborator

@robby81 - we're finally getting around to fixing some of the underlying incompatibilities with this. We're working on updating some of the internals of Funcotator and there will be a new datasources release very soon. After that I'll test this branch again to see if it's functional.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

6 participants