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Update README installation instructions
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... after removing mamba from the Bioconda recipe, installation
instructions should explicitely state that it is required for cluster
mode.

Also: Now using the most recent R version for pinning (R 4.0.3 is marked
broken in anaconda).
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Marius Wöste committed Oct 19, 2021
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16 changes: 6 additions & 10 deletions README.md
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Expand Up @@ -13,22 +13,18 @@ To run `wg-blimp` you need a UNIX environment that contains a [Bioconda](http://
It is advised to install `wg-blimp` through Bioconda. It is **strongly** recommended to install `wg-blimp` in a fresh environment, as it has many dependencies that may conflict with other packages, for this you can use:

```
conda create -n wg-blimp wg-blimp r-base==4.0.3
conda create -n wg-blimp wg-blimp r-base==4.1.1
```

***WARNING***: Installing wg-blimp will install mamba and conda as a dependency, so make sure to not install `wg-blimp` in an environment that is used for other purposes, and always run `conda deactivate` after running `wg-blimp`.Otherwise you might accidentally use the `conda` version installed by `wg-blimp` instead of your own.
***WARNING***: You need to install `mamba` as well if you intend to use `wg-blimp`'s cluster mode (e.g. on SLURM clusters) using the following command:

### Docker

We bundled a full `wg-blimp` installation into a Docker container. You may pull our image using
```
docker pull imimarw/wg-blimp:v0.9.8
conda create -n wg-blimp wg-blimp r-base==4.1.1 mamba
```

Once the image was downloaded and extracted, you can start the docker container with
```
docker run -it -v <directory-to-be-mounted>:<mounted-directory-in-container> imimarw/wg-blimp:v0.9.8
```
However, this will install `mamba` and `conda` as a dependency, so make sure to not install `wg-blimp` in an environment that is used for other purposes, and always run `conda deactivate` after running `wg-blimp`.
Otherwise you might accidentally use the `conda` version installed along `mamba` instead of your own.


### From source
You can also install `wg-blimp` from source using
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