Hi,
I've been trying to follow Cut&Run tools 2.0 pipeline.
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:
- https://conda.anaconda.org/conda-forge/win-64
- https://conda.anaconda.org/conda-forge/noarch
- https://conda.anaconda.org/bioconda/win-64
- https://conda.anaconda.org/bioconda/noarch
- https://repo.anaconda.com/pkgs/main/win-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/win-64
- https://repo.anaconda.com/pkgs/r/noarch
- https://repo.anaconda.com/pkgs/msys2/win-64
- https://repo.anaconda.com/pkgs/msys2/noarch
Any solution to this?
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.
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.