Galaxy

Connect to Galaxy for the first time

The Galaxy instance http://galaxy.sb-roscoff.fr needs an account. To get your login and password fill this form : "Account request".

The Galaxy instance http://webtools.sb-roscoff.fr does not need an account.

Upload a number of files < 2 GB

If you have a small number of files of less than 2 GB

Use this icon at the top-right of the tool panel (the left one)
Click and Drop your small files from your computer into the form

Upload many files or a file > 2 GB

Follow the screencast directly on the Galaxy frontpage in the Tutorials section or click on this [pdf]

Transfert files from the cluster /nz filesystem

 $ ssh ssh.sb-roscoff.fr
 $ cdprojet
 $ cd my_data_directory
 $ ftp galaxy3.sb-roscoff.fr
 Name (galaxy3.sb-roscoff.fr:lecorguille):
 331 Password required for lecorguille
 Password:
 230 User lecorguille logged in
 ftp> put fastq1.fq.gz
 ftp> put fastq2.fq.gz
 ftp> quit

Your datasets are now available in

Choose FTP file

Data life cycle

To optomize the storage capacity of our servers, it is important to regularly delete data that are no longer useful. Thus, to do this, please follow those following advices:

In Galaxy:

History panel:
1. Delete datasets
2. "Purge Delete Datasets" (through the wheel at the top-right of the history panel)
Saved Histories list:
1. "Delete Permanently" instead of "Delete"

On the server:

Physically delete files you uploaded on the server using your favorite SCP/FTP software client (cf. "Upload your files from your computer to the server")

Histories and workflows import/export

History

Currently, Galaxy does not allow history transfert between different Galaxy instances.

But you can download an archive of your datasets :

Click on the wheel at the top-right of the history panel
Export to file -> a link is proposed (please wait until the compression is done)
Use this link to download the archive or import it to another Galaxy server

Workflows

On the Galaxy Worflow tab, click the workflow you want to export and select Share or Download
On the new page, click the Download button in the Export section and save the file to your computer.
On the Galaxy Worflow tab, click the Upload or import workflow button at the top right
Click the Browse ... button and select the previously downloaded file.
Finish by clicking the Import button.

Tutorials and screencast

Galaxy is used in several projects and in many fields.

A video on the use of workflows for data analysis in metabolomics.
A video on the workflow set up within the framework of the PELAGOS project for analyzes of data using the R language within the Galaxy environment.

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Galaxy