Conda documentation #408
Conda documentation #408
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| Note that with conda installation you can't invoke the pipelines directly via Nextflow, so you will need to use the corresponding `cmat` commands - e.g. `cmat annotate` instead of `nextflow run annotation_pipeline.nf`. | ||
| All the same command line options apply. |
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Should we make this our main mode of executing CMAT ?
It sounds more elegant and easier to document.
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Assuming you mean just here in the readme, yes probably, I was just being lazy... I'll update.
I think it would also work for our OT submissions, I wanted to try getting the commands to work outside of the conda install but we could honestly even just use the conda version on our cluster...
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Is there somewhere the full list of corresponding cmat commands to use with conda?
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I've created #409 for generalising the wrapper script (and hence the short cmat commands), for now as you've suggested I've just included the corresponding cmat commands in the readme.
| - biopython ==1.77 | ||
| - coverage ==6.5.0 | ||
| - coveralls ==3.3.1 | ||
| - jsonschema ==3.2.0 | ||
| - numpy ==1.24.3 | ||
| - pandas ==1.5.3 | ||
| - pytest ==7.2.2 | ||
| - pytest-cov ==2.10.0 | ||
| - requests ==2.31.0 | ||
| - requests-mock ==1.8.0 | ||
| - retry ==0.9.2 |
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Is this some formatting standard I do not know about or an error ?
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It's a formatting standard that I also did not know about, bioconda utils lint picked it up in the PR.
| Note that with conda installation you can't invoke the pipelines directly via Nextflow, so you will need to use the corresponding `cmat` commands - e.g. `cmat annotate` instead of `nextflow run annotation_pipeline.nf`. | ||
| All the same command line options apply. |
There was a problem hiding this comment.
Is there somewhere the full list of corresponding cmat commands to use with conda?
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