Commit 480ef31b authored by Sarah Peter's avatar Sarah Peter

Use Ubuntu app on Windows, Anaconda shell does not work

parent bc6d17ba
......@@ -40,10 +40,7 @@ We will use conda on two levels in this tutorial. First we use a conda environme
### Windows
* Download and run the [Miniconda Windows installer](https://docs.conda.io/en/latest/miniconda.html) in the Python 3.7 version.
* Start "Anaconda Power Shell".
Alternatively, if you have 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, you can follow [these instructions](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. 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.
### MacOS
......@@ -84,7 +81,7 @@ $ source ~/.bashrc
```
After validation of the creation step and once activated, 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.
3. (MacOS and Linux only) Make sure Python does not pick up packages in your home directory:
3. Make sure Python does not pick up packages in your home directory:
```bash
(bioinfo_tutorial) $ export PYTHONNOUSERSITE=True
......@@ -138,13 +135,13 @@ and download the necessary data:
* Linux:
```bash
$ wget "https://webdav-r3lab.uni.lu/public/biocore/snakemake_tutorial/snakemake_tutorial_data.zip"
$ unzip snakemake_tutorial_data.zip
$ wget "https://webdav-r3lab.uni.lu/public/biocore/snakemake_tutorial/snakemake_tutorial_data.tar.gz"
$ tar -xzf snakemake_tutorial_data.tar.gz
```
* MacOS and Windows: Download the [zip file](https://webdav-r3lab.uni.lu/public/biocore/snakemake_tutorial/snakemake_tutorial_data.zip) from the WebDAV and unpack it into the directory we created above (normally `C:\Users\<your_username>\bioinfo_tutorial` on Windows and `/Users/<your_username>/bioinfo_tutorial` on MacOS).
* MacOS: Download the [archive file](https://webdav-r3lab.uni.lu/public/biocore/snakemake_tutorial/snakemake_tutorial_data.tar.gz) and unpack it into the directory we created above (normally `/Users/<your_username>/bioinfo_tutorial`).
Your working directory should have the following layout now:
Your working directory should have the following layout now (using the `tree` command):
```
.
......@@ -249,12 +246,6 @@ Create a file called `Snakefile` in the current directory and open it in your fa
$ open -a Textedit Snakefile
```
* Windows:
```bash
$ New-Item Snakefile -type file
$ Notepad Snakefile
```
Add the final rule for the mapping:
......@@ -305,7 +296,7 @@ s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load
19.1737 0:00:19 262.14 1404.55 258.79 258.94 0.00 0.00 0.00
```
After this step your working directory should contain the following files (using the `tree` command):
After this step your working directory should contain the following files:
```
.
......
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