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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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minor comments on the tutorial #215

Closed crsl4 closed 3 years ago

crsl4 commented 3 years ago

Hi Brant,

I am covering phyluce in my phylogenetics class and I found a couple of minor typos while following the tutorial step by step. In particular

  1. In the Install phyluce in its own conda environment, I had to do conda activate phyluce instead of source activate phyluce (similarly for deactivate). Not sure if this is Mac specific as I am using a Mac
  2. In the Clean the data, you have a cd my-analysis that should be cd uce-tutorial to be consistent with the rest of the steps
  3. Finally, I was unable to run trinity as they no longer support Mac. So maybe you can add this somewhere in the documentation. 
    NOTE: assemblo_trinity and Trinity are no longer supported on Mac OS.
Trinity has been consistently hard to build on Mac OS and we will no
longer be supporting it (unless it becomes easier to build).  We
suggest you use Trinity on Linux _OR_ ABYSS, itero, or spades on Mac
OS.

As I said, these are all minor things, so feel free to close the issue and ignore completely. Also, let me know if you prefer that I add these comments via a pull request.

Thanks for such a well-documented software!

brantfaircloth commented 3 years ago

Excellent - thank you! Changes made! Next steps (early summer) - finally finish updating everything for python3 and get all the software tests more reliably in-place...