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RADSex paper analyses workflow

Home Page: https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13360

License: GNU General Public License v3.0

Python 57.37% R 42.63%
analyses snakemake workflow

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paper-sexdetermination-radsex's Issues

radsex and sra-tools packages not found - error

Hello, I am attempting to use radsex to analyze ddRAD data. It is my intention to work through the workflow provided here before attempting to analyze my own data. I have complete the following steps:
(previous steps were homebrew and wget installation)

  1. wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

  2. bash Miniconda3-latest-MacOSX-x86_64.sh
    (Press enter until you can enter β€˜yes’ to agree)

  3. source ~/.zshrc

  4. conda init zsh

  5. conda update conda

  6. Create a new empty environment called "snakemake"

conda create --name snakemake

  1. Activate the environment "snakemake"

conda activate snakemake

  1. Install snakemake from the Bioconda channel (conda-forge contains dependencies)

conda install -c conda-forge -c bioconda snakemake

  1. Close and restart terminal

  2. use ssh to clone the repository

git clone https://github.com/RomainFeron/paper-sexdetermination-radsex.git

  1. navigate to the workflow's directory:
    cd paper-sexdetermination-radsex

  2. Activate snakemake
    conda activate snakemake

  3. Run Snakemake with jn cores (n = # of cores to dedicate)below
    snakemake -j2 --use-conda --restart-times 3

I get the following error (a colleague attempted to trouble-shoot with me and also got this error at this point)

(snakemake) jwiggi@LSW211-JoWigg paper-sexdetermination-radsex % snakemake -j2 --use-conda --restart-times 3
Building DAG of jobs...
Creating conda environment envs/workflow.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /Users/jwiggi/repos/paper-sexdetermination-radsex/rules/../envs/workflow.yaml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

ResolvePackageNotFound:

  • radsex=1.1.2
  • sra-tools=2.10.3

File "/Users/jwiggi/miniconda3/envs/snakemake/lib/python3.9/site-packages/snakemake/deployment/conda.py", line 387, in create

I've previously installed radsex using
conda install -c bioconda radsex

(snakemake) jwiggi@LSW211-JoWigg paper-sexdetermination-radsex % which radsex
/Users/jwiggi/miniconda3/envs/snakemake/bin/radsex

Could you please help me troubleshoot?

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