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Unable to create new environment in Conda for Cut&Run Tools 2.0

Hi,

I've been trying to follow Cut&Run tools 2.0 pipeline.

Cut&Run tools 2.0 Github

I've downloaded the install folder from the github page and run:

(base) D:\Adrian\Codes\CutRunTools2 Install packages>conda env create --file environment1.yml

Collecting package metadata (repodata.json): done Solving environment: failed

ResolvePackageNotFound:

  • bioconda::bedtools
  • macs2
  • bioconda::bedops
  • bioconda::samtools
  • bioconda::bowtie2

I do have the default bioconda channels created:

(base) D:\Adrian\Codes\CutRunTools2 Install packages>conda config --show channels

channels:

  • conda-forge
  • bioconda
  • defaults

Somehow my conda fails to search or install samtools or other related packages:

(base) D:\Adrian\Codes\CutRunTools2 Install packages>conda install samtools

Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  • samtools

Current channels:

Any solution to this?

bioconda conda anaconda
• 2,079 views • link
updated by Ram Ram • written by Adrian • Adrian

1 answer

samtools does not exist on conda for Windows. You should be using WSL2 to get a native Linux partition going. Bioinformatics on a pure Windows machine without WSL2 is going to be either a pain or impossible.

• 0 views • link
written by ATpoint ATpoint

Thanks for the input, ill try it out!

Sorry I'm a complete newbie at coding, but is WSL2 able to handle simple pipelines for bulk RNAseq and Cut&run? I'm just aiming to do the routine QC, trimming, normalization, mapping and simple output such as DEG / distribution heatmap / SAM or BAMs.

• 0 views • link
written by Adrian • Adrian

WSL2 powers a native Linux environment. You can do anything on it as you would on a "normal" Linux machine, so yes that is all possible. I do almost all my work in a WSL2 environment. DEG analysis is probably done in R though, you can power R either via WSL2 or via Windows directly, choice is yours.

• 0 views • link
written by ATpoint ATpoint

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