On Fri, Mar 23, 2012 at 10:45 PM, Luciano Cosme <cosme.sim...@gmail.com> wrote:
> Howdy,
>    Thanks Jen, I will try it tomorrow.
>
>    I installed Blast2Go from the Toolshed in my local instance of Galaxy and
> when I try to run it I get the following error:
>
> Index file named 'blast2go.loc' is required by tool but not available.
>
>    I logged as admin and the installation did not gave me any error. From
> the terminal:
>
> galaxy.util.shed_util DEBUG 2012-03-23 17:23:37,088 Installing repository
> 'blast2go'
> galaxy.util.shed_util DEBUG 2012-03-23 17:23:37,088 Cloning
> http://testtoolshed.g2.bx.psu.edu/repos/peterjc/blast2go
> destination directory: blast2go
> requesting all changes
> adding changesets
> adding manifests
> adding file changes
> added 2 changesets with 6 changes to 3 files
> updating to branch default
> 3 files updated, 0 files merged, 0 files removed, 0 files unresolved
> galaxy.util.shed_util DEBUG 2012-03-23 17:23:42,798 Updating cloned
> repository to revision "7b53cc52e7ed"
>
>
>    Anyway, I was thinking to use it because most of my differentially
> expressed genes are unknown. I was thinking to use Blast2GO to get them at
> least clustered in functional groups. I am not sure if that would be the
> best approach to find what might be the function of these genes. I also
> checked the list of public services that might have this tool, and Berkeley
> BOP is listed, but it seems that they no longer have the server or it was
> down when I checked (or the link is broken http://galaxy.berkeleybop.org/).
>
>
> Thank you.
>
> Luciano

Hi Luciano

The Galaxy team normal direct questions about local Galaxy
installs to the galaxy-dev mailing list (CC'd).

Have you seen the README file that comes with the
Blast2GO wrapper? Perhaps the 'install from toolshed'
could be tweaked to make this kind of documentation
more visible...

In order to use the Blast2GO wrapper in Galaxy you must
first install b2g4pipe (Blast2GO for pipelines) and create
your own blast2go.loc based on the blast2go.loc.sample
given. You will probably also want to install a local Blast2GO
database. None of that can be automated at the moment.

The blast2go.loc file is a list of Blast2GO profiles, which
can be used to set configuration options like weights and
thresholds. The primary use is to set the database, so
you can have an entry for the public database in Spain,
or an entry for a local database which would be MUCH
faster.

For example, locally we have Blast2GO in our Galaxy
with three databases right now - our local one which
is fast, and the recent and latest public databases
in Spain (which are comparatively slow because of
all the network access required).

Peter

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