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juliema / aTRAM

BSD 3-Clause "New" or "Revised" License
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an alternative way for installation was setted up #280

Closed Ulises-Rosas closed 4 years ago

Ulises-Rosas commented 4 years ago

Paths for scripts were updated inside the setup.py file. On this new version, users can also install dependencies by using a conda environment.

rafelafrance commented 4 years ago

I think we crossed paths on the review. Please see if my previous comments make sense and we can go from there.

rafelafrance commented 4 years ago

Minor edits based upon your suggestions will be made now.

Ulises-Rosas commented 4 years ago

Yes to requiring python3.

No to the pip from another repository. Atram is already a bit of a mess with all external the installs and I want to limit the external dependencies. Your original commit was working in this direction. Let's just tweak your original idea.

Is there a reason why you would not want to do this?

name: aTRAM
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - python=3
  - biopython
  - numpy
  - psutil
  - blast
  - velvet
  - trinity
  - abyss
  - spades
  - exonerate

not really, but if you consider to reduce dependencies, install directly from the repo will let you focus (i.e. update working) more in files which matters (e.g. setup.py or requirements.txt) instead of the environment.yml file. The prior is aplicable at least for python dependencies.