adds jasmine - Githubissues

Kincekara commented 3 months ago

PacBio movie files with kinetics are too big for tests. I couldn't find a downsampled test data. So, the test stage only calls jasmines' help. PacBio distributes this as pbjasmine.

Pull Request (PR) checklist:

[x] Include a description of what is in this pull request in this message.
[x] The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
[x] Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
- [ ] (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
[x] Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
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[x] Dockerfile includes the recommended LABELS
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Kincekara commented 3 months ago

related #926

erinyoung commented 3 months ago

Thanks for the PR! Since we can't test it via github actions, I'd like to test it locally before we deploy the image.

Do you have some test files and some example commands I should use?

Kincekara commented 3 months ago

https://downloads.pacbcloud.com/public/Sequel-II-CpG-training/CCS/methylated/

jasmine movie.hifi_reads.bam out.bam -j 16 --log-level INFO

@erinyoung the file is 18G. I tried to use this data with a staged test but failed because of the cache size. As an alternative to an external test, we can put a downsampled test file to github which will be ~30K for 1 read or ~300K for 10 reads. What do you think?

erinyoung commented 3 months ago

I think a downsamples bam file would be great.

We currently have some fastq and bam files in https://github.com/StaPH-B/docker-builds/tree/master/tests. You can put your test files there or in the jasmine subdirectory.

Kincekara commented 3 months ago

I removed the original file in the downsampling stage and it worked. I am leaving this image like this for now. If I hit a similar problem, I will add a test file next time.

erinyoung commented 3 months ago

The test works great!

#15 [test 2/2] RUN jasmine test.bam out.bam --log-level INFO
#15 0.173 | 20240515 16:34:52.469 | WARN | Model (5mC) chemistry (S/P5-C2/5.0-8M | R/P1-C1/5.0-25M) differs from data chemistry (S/P4-C2/5.0-8M)
#15 0.285 | 20240515 16:34:52.580 | INFO | 10 reads / 80.3 KBases
#15 0.285 | 20240515 16:34:52.581 | INFO | Reads      : 10
#15 0.285 | 20240515 16:34:52.581 | INFO | Yield      : 80.3 KBases
#15 0.285 | 20240515 16:34:52.581 | INFO | Throughput : 48.2 MBases/min
#15 0.285 | 20240515 16:34:52.581 | INFO | Run Time   : 186ms 651us 
#15 0.286 | 20240515 16:34:52.581 | INFO | CPU Time   : 83ms 973us 
#15 0.286 | 20240515 16:34:52.581 | INFO | Peak RSS   : 0.040 GB

Kincekara commented 3 months ago

@erinyoung I have added the pbdk version. I think this is ready to merge.

erinyoung commented 3 months ago

You can check the status of the deploy here: https://github.com/StaPH-B/docker-builds/actions/runs/9198414344

Thank you for putting this together!

StaPH-B / docker-builds

adds jasmine #978