1. Access Galaxy

Open http://galaxy.csb.univie.ac.at in your webbrowser and you will be presented with the Galaxy login screen. When accessing the site for the first time you will have to choose a username and a password of your choice, which are used for further logins. Upon logging in you will be presented with the galaxy main page, which is composed of the tools pane on the left and the history pane on the right.

2. Run VarCap in Galaxy

VarCap currently uses paired end read files for variant calling, therefore you will need 2 reads files (forward and reverse) in FASTQ format and 1 reference genome file in FASTA format. In order to avoid false positives at low percentages VarCap is optimized and designed for use with Illumina paired end reads.

2.1 Bringing your data into Galaxy

In order to use your data within Galaxy, you will have to upload it first. Uploading is done via the Galaxy upload tool. Simply click on the "Arrow icon" on top of the tools pane to open it and select the files you want to upload. image upload icon
With the upload tool you can upload files up to 2 GB, gzipped files are supported, bigger files need to be uploaded via our FTP server (see below for instructions concerning the FTP upload). Click "Start" and your files will be uploaded and displayed in the history pane on the right. A green background indicates that the file was uploaded successfully and is ready to use.

FTP upload to Galaxy

To upload files bigger than 2 GB we provide an FTP server instance. Use an FTP client that supports FTPS (like Filezilla) and connect to galaxy.csb.univie.ac.at, on Port 21 (the transfer is encryptet after connection via TLS), with the same username and password used for the galaxy web login. When you finished uploading your files, you should be able to select them in the Galaxy upload tool via "Choose FTP file".

2.2 Import the VarCap workflow

Access the published workflows menu by selecting "Shared Data > Published Workflows" in the top pane. image shared data menu
Select the “Varcap” workflow and select "Import" from the context menu.

2.3 Run VarCap within Galaxy

Access the workflow menu by selecting "Workflow" in the top pane. image workflow menu
Select the "Varcap" workflow and select "Run" from the context menu. You are now presented with VarCaps run configuration, where step 1 to 3 configure the input datasets and therefore have to to be set by you. Configure the workflow to use the previously uploaded files, for step 1 and 2 select the forward and reverse read files, for step 3 select the reference genome file. We have provided meaningful default values for the remaining steps, thus no further configuration is needed. To finally run the workflow, scroll down and select "Run workflow", a green message indicates that the job has been submitted successfully. Check the history pane for job status information.

VarCap output files

When VarCap has finished, there will be the following 3 output files showing up in the history pane:

Galaxy is running!

Galaxy is an open, web-based platform for data intensive biomedical research. The Galaxy team is a part of BX at Penn State, and the Biology department at Johns Hopkins University. The Galaxy Project is supported in part by NHGRI, NSF, The Huck Institutes of the Life Sciences, The Institute for CyberScience at Penn State, and Johns Hopkins.