Make container compatible with Nextflow and Singularity #108
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- 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
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Ooh yes, a small one: note that |
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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