galaxy-usage.md

Before running your own analysis using the ADMIRE [web service](https://bioinformatics.mpi-bn.mpg.de), you should have the following files on your local desktop:

* a SampleSheet.csv file and
* file directories named after the assays Sentrix-ID containing two *.idat files per sample.

To reduce the amount of data to send to the web server, compress the folders containing the *.idat files. To do this, select all folders and use built-in solutions from Windows or Mac to create a file that ends with

* .tar.gz, .tgz - uses the tar compression together with gzip or
* .tar.bz2, .tbz2, .tar.bzip2

![Compress](img/compress.png)

Now register a user by selecting the *User* tab in the top panel of the ADMIRE web page, followed by a click on *Register*. Fill in your email address and choose a password and a public name.
You don't have to wait for a confirmation email and can work right out of the box. 

![Register](img/register.png)

By creating a user account, you'll also be granted access to your personal FTP space on the server. As a next step, upload the compressed idat files into your remote FTP space.
To do so, use any FTP client or Windows Explorers built-in capabilities to connect to the FTP server at ftp://bioinformatics.mpi-bn.mpg.de:

![FTP connection](img/ftp.png)

Now drag and drop the SampleSheet.csv and the compressed file you created earlier into the FTP space:

![Upload](img/upload.png)

Change back to the web server and use the *Upload Tool* (1) to select the *SampleSheet.csv* file (2) **only** and upload it by clicking on *Execute* (3).

![Upload2](img/upload2.png)

Now choose the *ADMIRE* tool from the toolbar (4) and fill in the file name of the compressed idat files.

![Admire](img/admire2.png)

As a last step, choose genomic regions of interest and (optional) gene sets (8).
Hit the **Execute** button to see ADMIRE in action (9).

![Execute](img/execute.png)