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README: notebooks and help
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 - further help for executing software either in-place
   or copying it into PATH
 - additional notebooks
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DrYak committed Feb 8, 2021
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Expand Up @@ -171,8 +171,33 @@ We recommend using conda to install them:
```bash
conda env create -f conda_cojac_env.yaml
conda activate cojac
# now run from the cojac directory
./cooc-mutbamscan --help
```

_cojac_ itself doesn't have a specific installer but you can copy its executables in your _PATH_ (so you can call them without specifying their location), e.g.: into the conda environment:

```bash
# activate the environment if not already active:
conda activate cojac
cp cooc-* ${CONDA_PREFIX}/bin/
cooc-mutbamscan --help
```

### Remove conda environment

You can remove the conda environment if you don't need it any more:

```bash
# exit the cojac environment first:
conda deactivate
conda env remove -n cojac
```

## Additional notebooks

The subdirectory [`notebooks/`](notebooks/) contains Jupyter and Rstudio notebooks used in the [publication](#citation).

## Upcoming features

- [ ] bioconda package
Expand All @@ -193,6 +218,7 @@ Long term goal:

#### Additional notebooks:

- [Lara Fuhrmann ![orcid]](https://orcid.org/0000-0001-6405-0654), [![github]](https://github.com/LaraFuhrmann)
- [Katharina Jahn ![orcid]](https://orcid.org/0000-0002-6983-4615), [![github]](https://github.com/jahnka)

#### Corresponding author:
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