On Wed, May 1, 2013 at 11:43 AM, Mike Dyall-Smith
<mike.dyallsm...@gmail.com> wrote:
> Hi Peter,
>
> In biolinux, I start galaxy by a clicking on an application icon.
>
> If I open the terminal and run the suggested command: $ sh run.sh | grep -i
> blast
> I get the following output (long):
>
> $ sudo sh run.sh | grep -i blast
> python path is:
> /usr/lib/galaxy-server/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg,
...
> Traceback (most recent call last):
> socket.error: [Errno 98] Address already in use
> ----------------------------------------------------------------------------------------------
> as might be expected from this output, it doesn't start up galaxy at
> localhost.

That usually happens if Galaxy is already running and is using the port.
The second Galaxy instance therefore can't grab the port and so won't start.

>
>>check is the read permissions on the BLAST database
>   Well, from the terminal, I have access to all those files. The permissions
> are all the same, e.g.
>    -rwxrwx--- 1      root       vboxsf   15721925 Apr 10 18:55
> nr.00.phd
>
>  Within galaxy, I can open them with the get data menu command.
>

That appears to mean only the owner (root) and members of the group
vboxsf can read the files. That may explain why BLAST can't use the
files.

The simplest option is to make the BLAST database files (and if
needed, the containing folder too) world readable, e.g.

$ sudo chmod a+r /media/sf_mikeds_bioinf/db/nr*

Alternatively check the group memberships. What user is Galaxy running
as? (One way to check would be via top or ps when Galaxy is running).
My guess is whatever user that is, they are not a member of the vboxsf
group. To fix this, you could add the Galaxy user to the vboxsf group.

Peter
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