Commit f4fce19f authored by Christian Tischer's avatar Christian Tischer

Update README.md

parent f63b7a91
......@@ -64,13 +64,13 @@ TODO
#### Prerequisites
- Make sure you are in the EMBL intranet
- You need a terminal with the `ssh` command. On Mac and Linux this is included, on Windows please install [git for windows](https://git-scm.com/download/win) which includes a ssh command client (choose *Run Git and included Unix tools form Windows Command Prompt* on installation).
- You need a terminal with the `ssh` command. On Mac and Linux this is included. On Windows please install [git for windows](https://git-scm.com/download/win) which includes a ssh command client (choose *Run Git and included Unix tools form Windows Command Prompt* on installation).
- Your data and jupyter notebooks must be on a group-share, e.g. (Linux: `/g/kreshuk`; Mac: `/Volumes/kreshuk`; Windows: `\\kreshuk\kreshuk` )
#### Log into cluster and start an interactive jupyter notebook with stardist environment
- Open a terminal window on your computer
- Log into the EMBL cluster by typing:
- Log into the EMBL cluster:
- `ssh EMBLUSERNAME@login.cluster.embl.de`
- Enter you EMBL password.
- Ask for an interactive job on a GPU node:
......@@ -82,9 +82,9 @@ TODO
- Activate conda:
- `source /g/almf/software/miniconda3/run_conda.sh`
- Activate the stardist environment
- conda activate stardist-gpu
- `conda activate stardist-gpu`
- Go to a folder containing your notebooks
- cd /g/FOLDER/WITH/NOTEBOOKS
- `cd /g/GROUP/FOLDER/WITH/NOTEBOOKS`
- Run jupyter notebook with the IP of the cluster node that you are currently on
- `jupyter notebook --ip $IP`
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