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more installation guidelines
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salbrec authored Jun 26, 2021
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Expand Up @@ -216,6 +216,12 @@ Due to the amount of machine learning models to be trained, SIMPA can take up to
sbatch slurm
```

SIMPA can also be used with `mpiexec`. This works already within the docker or with a classical conda installation. The following call runs with, for instance, 2 cores:
```
mpiexec -n 2 python SIMPA.py -b ./scExamples/H3K4me3_hg38_5kb/BC8791969_B-cell.bed -t H3K4me3
```
Additional non-standard hardware for such an execution is not required.

## Further installation guides

### Installation with Docker Desktop on Windows
Expand Down Expand Up @@ -254,7 +260,7 @@ First, install anaconda in case you do not have it in your linux machine. We rec

```
wget https://repo.anaconda.com/archive/Anaconda3-2021.05-Linux-x86_64.sh
bash Anaconda3-2020.11-Linux-x86_64.sh
bash Anaconda3-2021.05-Linux-x86_64.sh
```
Accept licence and installation requirements with "return" and "yes", but follow the instructions, you might like to change the directory for anaconda. After installation it is necessary to initialize conda:
Expand All @@ -270,8 +276,4 @@ conda env create -f conda_env.yml
conda activate simpa
```

Having an MPI installation on a Linux server or local Linux machine, SIMPA can also be used with `mpiexec`. The following call runs with 2 cores:
```
mpiexec -n 2 python SIMPA.py -b ./scExamples/H3K4me3_hg38_5kb/BC8791969_B-cell.bed -t H3K4me3
```
Additional non-standard hardware for such an execution is not required.

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