Skip to content

Commit

Permalink
Remove references to gene-TF in README
Browse files Browse the repository at this point in the history
  • Loading branch information
jordanc17 committed Jul 7, 2023
1 parent dff6ba2 commit d4ba231
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ This repository contains a [`snakemake`](https://snakemake.readthedocs.io/en/sta

## Overview:

Below is a DAG showing the rule dependencies in the `snakemake` pipeline. View the [`Snakefile`](https://github.com/settylab/geneTF/blob/main/workflow/Snakefile) to see details on each rule.
Below is a DAG showing the rule dependencies in the `snakemake` pipeline. View the [`Snakefile`](https://github.com/settylab/atac-metacell-utilites/blob/main/workflow/Snakefile) to see details on each rule.

![DAG of workflow](./dag.png)

Expand Down Expand Up @@ -244,9 +244,9 @@ For example, the following will run/re-run the `chromvar` rule and any of the al
```
snakemake --cores 1 chromvar --allowed_rules peak_tf compute_ins_chip prep_chromvar
```
When running this pipeline on an HPC system which uses `lmod` to load software, do not load snakemake as a module - this can cause conflicts where the Python version used by `snakemake` is the one provided by the module, not the `gene-TF` conda environment.
When running this pipeline on an HPC system which uses `lmod` to load software, do not load snakemake as a module - this can cause conflicts where the Python version used by `snakemake` is the one provided by the module, not the `atac-metacell-utils` conda environment.

To run using the snakemake version installed with `gene-TF`, make sure the `gene-TF` environment is active, then run the pipeline as follows:
To run using the snakemake version installed with `atac-metacell-utils`, make sure the `atac-metacell-utils` environment is active, then run the pipeline as follows:

```
python -m snakemake --cores 1 name-of-rule
Expand Down

0 comments on commit d4ba231

Please sign in to comment.