On Sat, Feb 18, 2012 at 10:40 PM, Mikal Ustad <mikal.e.us...@gmail.com> wrote:
> Hello,
>
> I am part of a senior project group at Northern Arizona University.  We are
> interested in adapting Galaxy for a project related to building image
> processing workflows.  The existing system that we are working with uses XML
> files to make system calls and describe the attributes for each tool,
> similar to how Galaxy tools work.
>
> Galaxy has many features that we were planning on implementing, but there
> are also quite a few that are not useful to our project.  We are wondering
> if there exists a bare bones build of the Galaxy framework that we could
> adapt to our specific needs.  We appreciate any feedback you may have.
>
> Thank You,
>
> Mikal Ustad

Cool - I actually suggested this as a possible usage of Galaxy at a
workshop recently, in that case pipelines for processing microscopy
images.

You'd start by editing the tool list provided to the users (see file
tool_conf.xml) and removing almost everything - the default
toolset is not going to be very relevant. That then is your 'bare
bones' Galaxy.

You'd then need to write Galaxy XML files for the tools you want
to use instead, and add them to tool_con.xml instead.

This will likely include defining several new image datatypes in
Galaxy - assuming you have some specialised ones.

Further potential refinements might include code for previewing
a very large image in the central pane - much like how Galaxy
shows just the start of very large text data files.

Also I recall from a similar discussion on the list in the past
that you might have to change a preference to allow importing
images into Galaxy. Originally this was blocked to stop the
public Galaxy server being used as an online image host!
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-July/006107.html

Whomever first uses Galaxy like this will have the hardest
time, but with enhancements incorporated into the main
code, and image tools shared on the Galaxy Tool Shed,
this could open up Galaxy to a whole new user base.

Regards,

Peter

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