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shebang and executable on run_snp_pipeline.py #17

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antunderwood opened this issue Jun 23, 2016 · 3 comments
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shebang and executable on run_snp_pipeline.py #17

antunderwood opened this issue Jun 23, 2016 · 3 comments

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@antunderwood
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antunderwood commented Jun 23, 2016 •
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Should run_snp_pipeline.py have the shebang #!/usr/bin/env python and be executable?
@antunderwood
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ditto prepare_reference.py? and others?

@ulfschaefer
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phenix.py has a shebang and is executable. The other scripts are reachable as a subcommand do phenix.py as in phenix.py run_snp_pipeline -h, etc. Therefore only phenix.py needs to be executable, I think.

@antunderwood
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Ah ok - in that case please can the doc needs be updated:
http://phenix.readthedocs.io/en/latest/Calling%20SNPs.html

alexjironkin pushed a commit that referenced this issue Jun 24, 2016
Updated documentation for calling SNPs to use phenix.py (#17)
f786474
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@antunderwood @alexjironkin @ulfschaefer