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StaPH-B / docker-builds

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
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[Container Request]: kronaTools (failing to complete github actions test) #632

Open hkunerth opened 1 year ago

hkunerth commented 1 year ago

What tool are you looking for and why?

kronaTools is a useful set of scripts that I'm currently using to create krona plots from kraken2 outputs.

I have built a working dockerfile and stored it in my fork of the StaPH-B/docker-builds repository, but I'm unfortunately running out of storage when I use github actions to test the container. The issue comes from this part of the kronaTools usage:

To use these tools, updateAccessions.sh must be run after installing. This will install the local accession-to-taxonomyID database, which uses about 16 GB of disk space and an additional 16 GB of scratch space during installation (at the time of this writing; it is always growing) and takes minutes or up to an hour to run. It can also be run later to keep the local database up to date with NCBI.

While I can run this locally, running it through github actions fails when it runs out of disk space. Is there a possible workaround so that I can create a pull request for this container?

kapsakcj commented 1 year ago

Hi Henry,

Unfortunately that storage requirement is too large for the free GH actions runners, it won't be feasible to include that portion in the test stage of the dockerfile.

In the past we've taken the approach of simply commenting out the lines of code with updateAccessions.sh etc. commands so that if someone wants to build the image locally (where they have ample storage) they can uncomment and build the image to test that functionality

Are there other ways to test kronaTools that does not require the large amount of disk space?

You can keep the tests simple as pulling up --help or --version options if they exist.

erinyoung commented 8 months ago

@hkunerth , I know it's been awhile, but did you want to share your Dockerfile?

Sometimes tools just can't be testing with GA and we provide exceptions by testing some things with our local computational resources.

hkunerth commented 8 months ago

Hey @erinyoung,

I could probably do that! I'm a lot more experienced with Docker builds now, so let me take a look at it again next week to see if there's any improvements I can make, and then I'll let you know if we want to try to test it locally.