Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Develop installation instructions/README #5

Open
gregorgorjanc opened this issue Mar 24, 2023 · 1 comment
Open

Develop installation instructions/README #5

gregorgorjanc opened this issue Mar 24, 2023 · 1 comment

Comments

@gregorgorjanc
Copy link
Member

We should write how to install all the required software, including snakemake, Python, phasing, mamba/conda environments with tsinfer, ... all versioned

For example, I ran this on my Mac to install some snakemake version

mamba create -c bioconda -c conda-forge -n snakemake snakemake-minimal                                                                                       

mamba activate snakemake
@hannesbecher
Copy link
Contributor

Yes, we should also export the environments that are used by the pipeline, like conda list -n myCoustomEnv --explicit > myCoustomEnv.txt. Can then save these inside the repo. For this one would have to go through the rules and see which ends are used.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@gregorgorjanc @hannesbecher