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Use pysam instead of samtools binary #4479

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merged 1 commit into from Aug 24, 2017

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@nsoranzo
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commented Aug 22, 2017

This will make it possible to remove the requirement of having samtools installed when testing tools, e.g. in the tools-iuc TravisCI setup: https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L59

This can be tested with planemo test of the tool https://github.com/galaxyproject/tools-iuc/blob/master/tools/bedtools/bedToBam.xml .

Use pysam instead of samtools binary
This will make it possible to remove the requirement of having `samtools`
installed when testing tools, e.g. in the tools-iuc TravisCI setup:
https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L59
@bgruening

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commented Aug 22, 2017

Magic! Looks so easy and will help so many people! Only question I have is if we should given a warning/error message when no pysam is available.

Thanks @nsoranzo!
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commented Aug 22, 2017

That'd be up to @jmchilton, who requested the try/except for the import 😛

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commented Aug 22, 2017

We could still issue a warning before we set pysam = None, right?

@dannon

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commented Aug 24, 2017

This looks good to me. Elsewhere in the codebase when we try/except and set lib=None, we fail not when the import fails, but when trying to use it fails.

@dannon dannon merged commit 001d94a into galaxyproject:dev Aug 24, 2017

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lgtm analysis: JavaScript No alert changes
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toolshed test Build finished. 579 tests run, 0 skipped, 0 failed.
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@nsoranzo nsoranzo deleted the nsoranzo:use_pysam_in_verify branch Aug 24, 2017

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