[GEN-1163] hotfix annotation tools

[rxu17]

Purpose: This PR fix uses a universal way to get the current directory of the script. Mainly needed because our nextflow script calls the python script (inside Genie repo) that calls the bash script inside the annotation-tools repo

Testing:

• Tested locally on genie pipeline
• Tested on nf-genie using rebuilt docker image that contains this fix, and process_maf runs all the way through

[thomasyu888]

🔥 LGTM! You will have to rebuild the GENIE repo. A push to master branch with a change in the readme would probably do it.

[rxu17]

🔥 LGTM! You will have to rebuild the GENIE repo. A push to master branch with a change in the readme would probably do it.

Since I have to release a new version of annotation-tools and update the main genie Dockerfile, did you want me to update the Dockerfile and push that to master directly?

[thomasyu888]

🔥 LGTM! You will have to rebuild the GENIE repo. A push to master branch with a change in the readme would probably do it.

Since I have to release a new version of annotation-tools and update the main genie Dockerfile, did you want me to update the Dockerfile and push that to master directly?

Ah I forgot about the fact that we tagged releases now. Yes feel free to open a PR directly to master and I'll review.

[rxu17]

Ah I forgot about the fact that we tagged releases now. Yes feel free to open a PR directly to master and I'll review.

To be safe, I'm going to wait until I am a part of the genieadmin DockerHub team (asking IT on Monday) so I could build and push the test docker and have the Nextflow Tower workflow pull that to run it on the test pipeline. I'm not 100% positive that running nextflow locally vs via Tower will resolve file paths the same way even though theoretically they should be the same. Also hopefully then just getting the test pipeline on Tower to run all the way through (no issues) will mean similar smoothness for production. Hopefully that delay is ok.

[thomasyu888]

Ah I forgot about the fact that we tagged releases now. Yes feel free to open a PR directly to master and I'll review.

To be safe, I'm going to wait until I am a part of the genieadmin DockerHub team (asking IT on Monday) so I could build and push the test docker and have the Nextflow Tower workflow pull that to run it on the test pipeline. I'm not 100% positive that running nextflow locally vs via Tower will resolve file paths the same way even though theoretically they should be the same. Also hopefully then just getting the test pipeline on Tower to run all the way through (no issues) will mean similar smoothness for production. Hopefully that delay is ok.

The delay is ok! But we're going to run into problems with dockerhub because we don't have any more seats. The fastest way would be to build and push to your own dockerhub repo. We need to push to GHCR so we avoid the whole dockerhub situation...

Edit: alternatively, pushing to the dev branch will trigger a different tag to be created. So you can use that.

[rxu17]

Tested on Nextflow Tower : Ran on test-bash branch of nf-genie which uses the docker container on my personal github (rxu153/test-nf-genie:latest) that checks out the gen-1163-hotfix-annotation-tools branch of annotation-tools to use. See successful run on process_maf here: https://tower.sagebionetworks.org/orgs/Sage-Bionetworks/workspaces/genie-bpc-project/watch/1HTXq5rHaAvab8

Side note: Not sure why the create_data_guide module is failing on the test pipeline? Is this expected

[thomasyu888]

Tested on Nextflow Tower : Ran on test-bash branch of nf-genie which uses the docker container on my personal github (rxu153/test-nf-genie:latest) that checks out the gen-1163-hotfix-annotation-tools branch of annotation-tools to use. See successful run on process_maf here: https://tower.sagebionetworks.org/orgs/Sage-Bionetworks/workspaces/genie-bpc-project/watch/1HTXq5rHaAvab8

Side note: Not sure why the create_data_guide module is failing on the test pipeline? Is this expected

Thanks for doing that - LGTM!

That is expected because it's missing a file here. We can add it to get a thorough run through https://github.com/Sage-Bionetworks-Workflows/nf-genie/tree/main/scripts%2Fdata_guide%2Fgenomic_profiles

PS. I appreciate the urgency, but please enjoy your weekend! We can pick this up next week.