Martin Senger <[email protected]>
[using also few slides from the presentations from the
Galaxy Developers Conference 2011]
What Galaxy can do... (or could do)
Show me where I can try for myself
What can we do to make our Galaxy better
...and what this is not
• a detailed tutorial how to use Galaxy
• a way to convince you that I understand
everything about Galaxy
A web-based interface to the command-line tools
(of any kind) and their combinations
Galaxy performs analysis interactively through the web,
on arbitrarily large datasets
 Galaxy remembers what it did - history
Flexibility to include anybody’s command-line
by writing wrappers whose templates are available
An environment for sharing tools (or their
“Tools Shed” repository
Locally stored data
 shared between users
 e.g. genome builds
Origin of data
uploaded data from your computer
 using a web interface
 using an FTP server
fetched from external databases (“datasources”)
 only those that are “aware” of Galaxy
 internally: two ways how to fetch data (async vs. sync.)
 you need to be familiar with these databases and their UIs
• Data have metadata
• allowing to use
data only for those
tools that
recognize such
data types
• Data have attributes
• annotate data
• convert data to a
new format
• change data type
Automated set of steps – perhaps each time
with different input data (of the same type)
reproducibility (usable in publications)
 reusability (sharing workflows with others)
 created from the scratch (using a workflow editor) or
from your history
An example – a workflow
Thanks to:
user would not have done this from the command line on our
• If we have time (6mins) click here:
• Creating a workflow from your history
Where are all these galaxies?
public servers
 available immediately, free of charge
 and few others, such as
 usually limited resources
 you cannot customize them to your special needs
 running on an internal cluster with limited resources
 but we can do with it whatever we need to do
Galaxy in the Amazon clouds (CloudMan)
when you do not have infrastructure in house
when you have particular resource (cores, memory...) needs
when you need a customization
if you have a credit card
details in this presentation:
Galaxy has also the RESTfull API for programmatic access (beta)
...we need to:
Image courtesy of
Data issues
make a subset of tools we really need and test them fully
consider to wrap other tools (not yet available by default)
add genome-wise data we (CBRC) need
add data usable for others (Core, students...)
provide user-oriented courses
create a user group to share experience and to promote knowledge
monitor its stability and usage
Hardware/sysadmin issues
Install it on better hardware (in due time)
Change the current queue priority (a chicken-egg problem)
Add an ftp server
Galaxy home page:
An overview presentation: