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Fix slurm install instructions #294

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Aug 14, 2024
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Fix slurm install instructions #294

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19 changes: 10 additions & 9 deletions docs/installation.md
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Expand Up @@ -165,33 +165,34 @@ docker run -v $DATA_FOLDER:/app/data/ --rm alphadia-docker

### 1. Set up environment
Check if conda is available on your cluster. If not, install it, or, if provided, load the corresponding module, e.g.
`module load anaconda/3/2023.03`.
`module load anaconda/3/2023.03`. You might be asked to run `conda init bash` to initialize conda.

Create and activate a new conda environment
```bash
conda create -n alphadia python=3.11
conda create -n alphadia -y
conda activate alphadia
```
### 2. Installing mono
Install mono to support reading proprietary vendor formats like Thermo `.raw` files.

Please make sure you include the conda-forge channel

Install python into your new environment
```bash
conda install python=3.11 -c conda-forge
conda install python=3.11 -y
```
Then install mono by
```bash
conda install mono -c conda-forge
conda install mono=6.12.0.182 -c anaconda -y
```

Make sure mono is installed by running
Test that mono is correctly installed by running
```bash
mono --version
```

Make sure the output looks something like this:
The output should look something like this:
```
Mono JIT compiler version 6.12.0.90 (tarball Fri Mar 5 04:37:13 UTC 2021)
Mono JIT compiler version 6.12.0.182 (tarball Mon Jun 26 17:39:19 UTC 2023)
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com
TLS: __thread
SIGSEGV: altstack
Expand All @@ -212,7 +213,7 @@ Install alphaDIA using pip:
```bash
pip install "alphadia[stable]"
```
Afterwards, verify the alphaDIA installation by running:
Afterward, verify the alphaDIA installation by running:
`alphadia --version` which should output the current version.

### Notes on running alphaDIA as part of automated workflows
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