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Update documentation
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CharlieLaughton committed Nov 20, 2023
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10 changes: 5 additions & 5 deletions Session_2/Preparation.md
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Expand Up @@ -14,12 +14,12 @@ ssh <username>@login.archer2.ac.uk

The instructions here are adapted from those in the [Archer2 User Guide](https://docs.archer2.ac.uk/user-guide/).

It's important you create the virtual environment in your personal `/work` folder, not in your home directory. This is `/work/<projectname>/<projectname>/<username>` - here we assume `<projectname>` is *e280* :
It's important you create the virtual environment in your personal `/work` folder, not in your home directory. This is `/work/e280/e280/<username>`:

```bash
module load cray-python
python -m venv /work/e280/e280/<username>/myvenv
source /work/e280/e280/<username>/myvenv/bin/activate
python -m venv /work/e280/e280-workshop/<username>/myvenv
source /work/e280/e280-workshop/<username>/myvenv/bin/activate
```

### Step 3 (on Archer2): Install the required Python packages
Expand Down Expand Up @@ -62,7 +62,7 @@ module load cray-python
module load gromacs
module load autodock-vina-1.2.5
module load openbabel-3.1.1
source /work/e280/e280/crossflow001/myvenv/bin/activate
source /work/e280/e280-workshop/<username>/myvenv/bin/activate
```

Log out of Archer2 and then back in again. You should find you are back in your virtual environment, and each of the following commands should give some output:
Expand All @@ -77,7 +77,7 @@ which obabel

Move to your work directory:
```bash
cd /work/e280/e280/<username>
cd /work/e280/e280-workshop/<username>
```
And use a text editor to create a shell script `jstart.sh` containing:

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