Conda env

[leebrian]

Thanks for posting this. I learned a lot by seeing how you wrote this pipeline.

If convenient, would you add the conda env file to this project? Seeing the dependencies and configurations will make it a little easier to follow and emulate.

[kapsakcj]

Thanks for sharing this script! This will script will really help to serve as a model if I write any bioinfo pipelines in a python script!

I second the notion that you add a conda env file 😄

Lingzi also requested to be kept in the loop about this since she's interested in trying out pima as well.

[chrisgulvik]

The basecaller guppy is only available at their website, so that installation must be done on your own. I just added a pull request (README.md update) to show how you can create a conda env that handles most of the other dependencies. If you invoke --plasmids (default is off), then pblat is needed (also missing from conda) and the R I left out but could be done with conda install blat circos r-hash r-stringr