Hi all,
When running galaxy-dist/run_reports.sh I get errors. It has been awhile
since I run it, and it worked perfect then however.
python path is:
/home/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg,
/home/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x
Hi Joachim
I suggest you double check the settings in "reports_wsgi.ini"
One of your error messages: "sqlalchemy.exc.OperationalError:
(OperationalError) could not connect to server: Connection refused"
indicates that there is something wrong with the value for
"database_connection".
And yo
Thanks, Hans. I found that the problem lies somewhere else... I was
trying to mount a systems temporary directory (/tmp) on an NFS share.
The socket to the postgres database however (although sync'ed to the NFS
share) was apparently not valid anymore on the NFS share.
I unmounted /tmp again (t
On Aug 29, 2012, at 12:41 PM, Douglas W Cloud wrote:
>
> Hello all,
> I am trying to get a Galaxy server configured to submit jobs to an
> LSF cluster running version 7 update 2, generally CentOS/Redhat 5 systems.
> I have the Galaxy host as a client in LSF, but when I tried to
> configure/
Hi,
I just added a new tool to my existed work flow. And I would like to set
the parameter of this tool to 'set at runtime', but I got an error message
as following:
Server error
URL: http://127.0.0.1:8085/workflow/editor_form_post
Module weberror.evalexception.middleware:*364* in respond
>>
On 29 August 2012 21:11, Nate Coraor wrote:
> On Aug 24, 2012, at 9:48 AM, Mutlu Dogruel wrote:
>
> > Hi folk,
> >
> > Do you know any method for reading (the extended) WSGI HTTP headers
> > from a custom tool?
> >
> > If I put some debugging lines in
> > $galaxy/lib/galaxy/web/framework/middlewa
The cloud admin interface's automatic update mechanism doesn't currently
support toolshed updates due to the interaction required. At this point, if
you're updating a cloud instance you'll need to do it manually. SSH in, switch
to the galaxy user, navigate to /mnt/galaxyTools/galaxy-central, a
Dear Galaxy Developers,
First, thanks for the great work. Galaxy is a amazingly well architected and
extraordinary useful system.
Of course, I have a feature request to make it even more perfect ;-) The list
of tool sections is already very long. It would be nice to organize the
sections in n
I have been using the FreeBayes tool in our local Galaxy instance for
some time. As FreeBayes is a rapidly evolving tool, it has been very
helpful to have Daniel Blankenberg work on keeping an updated wrapper.
Recently, I've run into a rather troublesome bug in FreeBayes
(https://github.com/e
On Jul 23, 2012, at 11:02 AM, Steven Peckins wrote:
>
> I've been asked to set up a local Galaxy installation specifically for
> large datasets (tens of terabytes).
>
> Is there a list of default locations where Galaxy puts data? As an admin,
> that would be my first question, but it's not obvi
Hi, Galaxy Developers,
This is just a follow up to my previous response; I was able to get things
working, and have pasted our apache configuration below for anybody else that
search the mailing list with similar problems. Our implementation
authenticates against UNIX LDAP and use a group fo
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