[mira_talk] Re: Run MIRA in Galaxy....

  • From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 8 Dec 2011 12:03:05 +0000

On Thu, Dec 8, 2011 at 6:37 AM, Manju Rawat <manju.rawat2@xxxxxxxxx> wrote:
> Hello,
> Is there anybody who can help me to run MIRA in Galaxy....
> I have installed the MIRA in my ubuntu system and its working fine..and i
> want to run it in my local Galaxy...
> I have downloaded the mira.py,mira.txt and mira.xml from the Galaxy tool
> shed....
> Thanks
> Manju Rawat

Hi Manju,

I wrote the MIRA wrapper for Galaxy, which I assume you've
found via the Galaxy Tool Shed, http://community.g2.bx.psu.edu/

This is probably better answered on the galaxy-dev mailing
list. Have you ever installed a Galaxy Tool before? I can
talk about the "old fashioned" way to do this - but the
Galaxy team have been working to make installing tools
from the Tool Shed much more automated. The manual
way, which is described briefly in the mira.txt file is as

1. Ensure the tool dependencies are on the PATH,
in this case ensure mira is on the path.

2. Put the mira.xml and mira.py (and mira.txt) files
under your Galaxy tools folder, in this case use:

3. Edit your tool_conf.xml to add this line at a
sensible point in the tool menu,
<tool file="sr_assembly/mira.xml" />

4. Restart Galaxy.

I should point out that MIRA literally has hundreds of
options, while the Galaxy wrapper deliberately keeps
this very simple and essentially only covers the defaults.

Note the wrapper doesn't yet support Ion Torrent data,
but that would be fairly easy to add.

Also, please head the warnings in mira.txt about the
computational needs of MIRA and if you Galaxy
server/cluster can cope with it.


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