add busco-prok with bacteria_odb #854
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
@erinyoung, do you want any more changes to this image? I left this as a draft for now. |
erinyoung
reviewed
Jan 25, 2024
| # offline test | ||
| RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/941/835/GCA_010941835.1_PDT000052640.3/GCA_010941835.1_PDT000052640.3_genomic.fna.gz && \ | ||
| gzip -d GCA_010941835.1_PDT000052640.3_genomic.fna.gz && \ | ||
| busco --offline -l bacteria_odb10 -m genome -i GCA_010941835.1_PDT000052640.3_genomic.fna -o offline --cpu 4 && \ |
There was a problem hiding this comment.
I like that you include an offline test to make sure that it's working
|
I think this looks great! I don't have any changes to recommend, except for adding it to the main readme. I think it's okay if the other, smaller version being the default 'latest' tag. |
erinyoung
approved these changes
Jan 25, 2024
|
I couldn't find a name that is short and definitive, unfortunately. If you have something in your mind, we can change it. |
|
Alright. I'm going to use that tag then. You can check the status of the deploy at https://github.com/StaPH-B/docker-builds/actions/runs/7660600410 Thank you for putting this together! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Closes #848
I left prokaryotes only tools to make a smaller image.
Busco uses the working directory to search and download lineage sets. So I added bacteria linage into the data folder.
Pull Request (PR) checklist:
docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15)spades/3.12.0/Dockerfile)shigatyper/2.0.1/test.sh)spades/3.12.0/README.md)