Commit 94c33375 authored by Sarah Peter's avatar Sarah Peter

Remove connection command, generalise rsync

parent 27ca096d
......@@ -20,14 +20,15 @@ It can encapsulate software and packages in environments, so you can have multip
We will use conda on two levels in this tutorial. First we use a conda environment to install and run snakemake. Second, inside the snakemake workflow we will define separate conda environments for each step.
1. Start a job on the cluster:
1. Connect to the cluster
2. Start an interactive job:
```bash
(laptop)$> ssh iris-cluster
(access)$> si
```
2. Install conda:
3. Install conda:
```bash
(node)$> mkdir -p $SCRATCH/downloads
......@@ -49,19 +50,20 @@ We will use conda on two levels in this tutorial. First we use a conda environme
(node)$> conda update conda
```
3. Create a new conda environment and activate it:
4. Create a new conda environment and activate it:
```bash
(node)$> conda create -n bioinfo_tutorial
(node)$> conda activate bioinfo_tutorial
```
You can see that your prompt will now be prefixed with `(bioinfo_tutorial)` to show which environment is active. For the rest of the tutorial make sure that you always have this environment active.
4. Install snakemake:
5. Install snakemake:
```bash
(node)$> conda install -c bioconda -c conda-forge snakemake-minimal
```
## Create snakemake workflow
......@@ -496,12 +498,17 @@ Now that we have completed the workflow, let's have a look at the results.
For visualisation, [download IGV](http://software.broadinstitute.org/software/igv/download), or use any other genome browser of your choice.
To copy the results from the cluster to your laptop, run the following and replace `<your_username>` with your ULHPC user login. Pay attention in which directory you are, so you can find the files again.
To copy the results from the cluster to your laptop, run the following in a local terminal (Linux and MacOS) or a MobaXterm local session (Windows) and replace `<your_username>` with your ULHPC user login. For alternative ways to transfer files, see the [documentation on the HPC website](https://hpc.uni.lu/users/docs/filetransfer.html). Pay attention in which directory you are, so you can find the files again.
```bash
(laptop)$> mkdir bioinfo_tutorial
(laptop)$> cd bioinfo_tutorial
(laptop)$> rsync -avz iris-cluster:/scratch/users/<your_username>/bioinfo_tutorial/output .
# check where you are
(laptop)$> pwd
# transfer the output directory
(laptop)$> rsync -avz --rsh='ssh -p 8022' <your_username>@access-iris.uni.lu:/scratch/users/<your_username>/bioinfo_tutorial/output .
```
Start IGV and select mouse mm10 as genome in the drop-down menu in the upper left. Go to "File" -> "Load from File…" and select all three files that you have copied from the cluster.
......@@ -587,4 +594,4 @@ With `squeue -u <your_username>` you can check the status of the submitted jobs
## Acknowledgements
Many thanks to Nikola de Lange, Aurélien Ginolhac, Roland Krause and Cedric Laczny for their help in developing this tutorial.
Many thanks to Aurélien Ginolhac, Cedric Laczny, Nikola de Lange and Roland Krause for their help in developing this tutorial.
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