romainferon / paper-sexdetermination-radsex Goto Github PK
View Code? Open in Web Editor NEWRADSex paper analyses workflow
Home Page: https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13360
License: GNU General Public License v3.0
RADSex paper analyses workflow
Home Page: https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13360
License: GNU General Public License v3.0
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)
wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
bash Miniconda3-latest-MacOSX-x86_64.sh
(Press enter until you can enter βyesβ to agree)
source ~/.zshrc
conda init zsh
conda update conda
conda create --name snakemake
conda activate snakemake
conda install -c conda-forge -c bioconda snakemake
Close and restart terminal
git clone https://github.com/RomainFeron/paper-sexdetermination-radsex.git
navigate to the workflow's directory:
cd paper-sexdetermination-radsex
Activate snakemake
conda activate snakemake
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:
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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