Commit e2b42078 authored by Sarah Peter's avatar Sarah Peter

Add instructions for VirtualBox

parent f563a2c3
......@@ -40,7 +40,21 @@ We will use conda on two levels in this tutorial. First we use a conda environme
### Windows
You need at least Windows 10 with the [Windows 10 Fall Creator update](https://support.microsoft.com/en-gb/help/4028685/windows-10-get-the-fall-creators-update), released October 2017. Use [this guide](https://tutorials.ubuntu.com/tutorial/tutorial-ubuntu-on-windows) to install the [Ubuntu app](https://www.microsoft.com/de-de/p/ubuntu/9nblggh4msv6?activetab=pivot:overviewtab) from the Microsoft Store. Then follow the Linux instructions.
You need at least Windows 10 with the [Windows 10 Fall Creator update](https://support.microsoft.com/en-gb/help/4028685/windows-10-get-the-fall-creators-update), released October 2017.
* Check that the Windows Subsytem for Linux is enabled: open "Control Panel" -> "Programs and Features" -> "Turn Windows Feature on or off" -> check "Windows Subsystem for Linux".
* Use [this guide](https://tutorials.ubuntu.com/tutorial/tutorial-ubuntu-on-windows) to install the [Ubuntu app](https://www.microsoft.com/de-de/p/ubuntu/9nblggh4msv6?activetab=pivot:overviewtab) from the Microsoft Store.
* Run the Ubuntu app and change the directory to a location that you can access from Windows:
```bash
$ cd /mnt/c/Users/<your_username>/
```
* Then follow the Linux instructions.
For older versions of Windows follow the [instructions to set up VirtualBox](virtualbox.md).
### MacOS
......@@ -137,6 +151,7 @@ Create a working directory and download the necessary data::
```bash
$ mkdir bioinfo_tutorial
$ cd bioinfo_tutorial
$ curl https://webdav-r3lab.uni.lu/public/biocore/snakemake_tutorial/snakemake_tutorial_data.tar.gz -o snakemake_tutorial_data.tar.gz
$ tar -xzf snakemake_tutorial_data.tar.gz
```
......@@ -491,7 +506,7 @@ TC1-ST2-D0.12_peaks.narrowPeak
TC1-ST2-D0.12_treat_pileup.bigwig
```
Snakemake can visualise the dependency graph of the workflow with the following command (Linux and MacOS with `dot` installed):
Snakemake can visualise the dependency graph of the workflow with the following command (if `graphviz` is installed):
```bash
$ snakemake --dag | dot -Tpdf > dag.pdf
......@@ -521,7 +536,7 @@ When you hover over the blocks in the `TC1-ST2-D0.12_peaks.narrowPeak` track, yo
## Useful stuff
*
* If `PYTHONNOUSERSITE` is set, Python won’t add the [`user site-packages directory`](https://docs.python.org/3/library/site.html#site.USER_SITE) to [`sys.path`](https://docs.python.org/3/library/sys.html#sys.path). If it's not set, Python will pick up packages from the user site-packages before packages from conda environments. This can lead to errors if package versions are incompatible and you cannot be sure anymore which version of a software/package you are using.
<a name="references"></a>
......
# Set up VirtualBox
## Install VirtualBox
## Import Ubuntu image
## Configure shared directory
## Configure SSH access from host
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