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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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"phyluce_snp_bwa_multiple_align" command missing in phyluce 1.7.1 #224

Open jasonleebrown opened 3 years ago

jasonleebrown commented 3 years ago

I am phasing some data and I have run into an issue (issue #205) where I couldn't get the step using "phyluce_snp_bwa_multiple_align" to work. In an effort to troubleshoot I have ran the example data in your tutorial (after my data didn't work). I received the same error using my old install. Then I installed a new version of phyluce v1.7.1. When I run the function "phyluce_snp_bwa_multiple_align" - it now states that the 'command not found'. I used other common commands to phlyuce and everything else appears to works. Is this command removed or replaced by something else? Thanks again for all your efforts here - this is an amazing accomplishment. Jason Brown

brantfaircloth commented 3 years ago

Hi Jason,

First, thanks! Second, it no longer exists. See the documentation on "workflows". The newer implementation is a bit more flexible on my end (and on the user end if you decide to make it so).

Also, if you are phasing, you'll be phasing using a workflow, too, and you'll need to see this bug report for the short term fix.

jasonleebrown commented 3 years ago

Thanks- will try it and update here if success if achieved.