Make container compatible with Nextflow and Singularity#108
Open
zwets wants to merge 6 commits intopha4ge:masterfrom
Open
Make container compatible with Nextflow and Singularity#108zwets wants to merge 6 commits intopha4ge:masterfrom
zwets wants to merge 6 commits intopha4ge:masterfrom
Conversation
- Add bash to container as Nextflow needs this to do its own business
- Replace forced ENTRYPOINT with soft CMD for Singularity and Nextflow
+ Note: running the container now needs 'hamronize' as first argument,
this was previously the implicit (and enforced) ENTRYPOINT
- Document in README the docker run ... invocation line
- Remove the (unneeded) licensed Conda 'default' channel in README
- Changed from one line per antimicrobial to one line per gene
Contributor
Author
|
Ooh yes, a small one: note that |
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Hi Finlay,
These changes make the container produced by the
Dockerfile:ENTRYPOINTbyCMD.The entrypoint removal has one noticeable consequence: running the container now needs
hamronizeas the first argument. Previously this wasn't needed becauseENTRYPOINTset this - and enforced it, to the dismay of Nextflow and Singularity (who want to run other things in the container, too).I have also added a sample
docker runinvocation line to the README, and a handful of typo and style fixes.Edit: sorry for piggybacking one more commit on this PR. It is a change to make ResFinder's hamronized output more like that of AMRFinderPlus and RGI. It now outputs one row per gene rather than per antimicrobial.
Best wishes,
Marco