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rkweku / miRador

Plant miRNA identification tool that utilizes a variety of filters to validate predicted miRNAs
GNU General Public License v3.0
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conda errors and installation clarifications #13

Open MikeAxtell opened 3 months ago

MikeAxtell commented 3 months ago

Hi Reza, I found some issues with using conda to install miRador dependencies that you may want to look at:

  1. conda create -n mirador -f environment.yml : This command fails with recent versions of conda because the -f switch is invalid. I believe it is --file on my system. I am running conda version 24.1.2 installed by miniconda for linux 64 centOS.
  2. Correcting the -f to --file also fails with error CondaValueError: could not parse 'name: mirador' in: environment.yml.
  3. For the alternative "step-by-step" conda instructions given in the README, after the conda create --name mirador step, users should then be told activate the environment by conda activate mirador. Otherwise, naive users may end up installing the dependencies into their base environment, or some other place where it doesn't belong. I suggest adding that step in to the README.
  4. Several of the "step-by-step" conda install commands will fail for users whose .condarc file sets channel priority to strict. Users of Bioconda will already have channel_priority set to strict because that is a requirement of Bioconda. To use your stated instructions, such users need to edit their .condarc file to set channel_priority to flexible (and then switch it back when done).
  5. The command conda install -c conda-forge ghostscript=9.54.0 perl=5.32.1 pypdf2=2.11.1 typing_extensions-4.5.0 has a typo that will cause it to fail. typing_extensions-4.5.0 should be edited to typing_extensions=4.5.0

Hope this helps, I'm looking forward to giving miRador a spin!

rkweku commented 3 months ago

Hi Mike,

I was going through this today and it seems I left out a critical part of the conda create command that should create the environment. It should actually be: conda env create -n mirador -f environment.yml

I'll update the README further to accommodate all of your suggestions. Thank you for all of these!

Reza