I am trying to install the mothur toolsuite via the toolshed but this
returns in an HTTP 500 error:
line 144 in __call__
app_iter = self.application(environ, sr_checker)
line 106 in __call__
line 543 in intercept_output
app_iter = application(environ, replacement_start_response)
line 84 in __call__
return self.application(environ, start_response)
line 633 in __call__
return self.application(environ, start_response)
line 160 in __call__
body = method( trans, **kwargs )
line 184 in decorator
return func( self, trans, *args, **kwargs )
line 451 in install_repository
clone_repository( repository_clone_url, os.path.abspath(
relative_install_dir ), ctx_rev )
line 286 in clone_repository
rev=[ ctx_rev ] )
line 1157 in clone
line 350 in clone
destrepo.clone(srcrepo, heads=revs, stream=stream)
line 2280 in clone
return self.pull(remote, heads)
line 1582 in pull
remotephases = remote.listkeys('phases')
line 115 in plain
line 163 in _submitone
return self._call(op, **args)
line 169 in _call
fp = self._callstream(cmd, **args)
line 117 in _callstream
resp = self.urlopener.open(req)
File '/usr/lib/python2.7/urllib2.py', line 397 in open
response = meth(req, response)
File '/usr/lib/python2.7/urllib2.py', line 510 in http_response
'http', request, response, code, msg, hdrs)
File '/usr/lib/python2.7/urllib2.py', line 435 in error
File '/usr/lib/python2.7/urllib2.py', line 369 in _call_chain
result = func(*args)
File '/usr/lib/python2.7/urllib2.py', line 518 in http_error_default
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
Any ideas how to fix this?
I try to use the visualization tool of my local instance of galaxy under
ubuntu. Everytime I try to create a feature track from a sam file, I get the
/bin/sh samtools not found
I have installed samtools from ubuntu reposotories and it works well as I can
call it from the shell. Nevertheless, I still get the same error.
I checked that the samtools binary is in a folder included in my $PATH as
I tried to use an "analyze data" tool in galaxy interface that uses samtools
and it worked.
It seems that it's only in trackster that samtools are not found.
Do you have an idea to fix it?
Plateforme Genome Transcriptome
Tel: 05 57 12 27 75
INRA-UMR BIOGECO 1202
69 route d'Arcachon
I am having an issue with getting the FastQC tool to work with Galaxy on
our server. I downloaded the FastQC files (version 0.8.0) and changed the
directory that the wrapper script looks for the 'fastqc' executable in, but
when we run a job with it we have been getting the following output:
"Started analysis of Clip
Approx 5% complete for Clip
Approx 10% complete for Clip
Approx 95% complete for Clip
Approx 100% complete for Clip
Analysis complete for Clip
(.:9754): Gtk-WARNING **: cannot open display: "
And then the job shows as failed in Galaxy. The output .dat file just has
that same output/error message in it (though it seems to indicate it got to
100%). Also when I try to execute the fastqc file directly (albeit with no
arguments) I get this:
"Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation
which requires it.
Both errors seem to have something to do with the graphical GUI component
of FastQC (which I have seen some screenshots for on the FastQC webpage).
If this application is GUI-driven how did the online PSU Galaxy get it to
work with their wrapper script when the tools are run in a command-line
environment with no X11 or Gtk? Essentially I'm just wondering what steps
I'm missing here to getting this to work with our Galaxy mirror, other than
just dropping the executable in place? Any suggestions?
On 7/1/12 3:05 AM, Katrien Bernaerts wrote:
> I am making a Galaxy appliciation with a text area. In the text area,
> the user can copy/paste sequences. However, all carriage returns (e.g.
> after the comment line) are converted to XX by Galaxy. I found that a
> sanitizer can be used for specal characters, but I could not figure
> out how to configure the sanitizer for a carriage return. Does anyone
> have an idea how to handle carriage returns in the user input?
> Thanks in advance,
> Katrien Bernaerts
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
-- Jennifer Jackson http://galaxyproject.org
The deadline to apply for the GMOD Summer School is in one week, July
9th. The application is available as a Google Form:
In the GMOD Summer School (August 24-29, 2012) we will cover the
installation, configuration and use of a variety of GMOD tools,
including Chado, GBrowse, JBrowse and Galaxy. For more information on
the course, see the course web page at
The course will make heavy use of the Amazon Web Service (aka, the
Cloud) via a grant from Amazon. Enrollment is limited to 24 students,
and the application process is competitive: the last few years we've
received over 75 applications for those 24 spots.
I look forward to seeing you in North Carolina in August!
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
I have added some tools to my local install of Galaxy. To get to my final results I have to do a lot of steps. When I try to run every step separately it turns out to work out fine. But when I try to run all steps at once with a workflow I get the following error message.
OperationalError: (OperationalError) database is locked u'UPDATE dataset SET update_time=?, state=? WHERE dataset.id = ?' ['2012-07-02 11:34:48.135419', 'queued', 529]
I have noticed that the processes eat a lot of my computer resources. Other than that I have no clue what the problem could be.
Any tips are appreciated.
Jaap van der Heijden
I have updated our development installation of Galaxy. This wasn't done for a long time, so it was a quite old version.
The update is done from galaxy-central.
I did hg pull, hg update and a db update. All that without errors.
But when I now try to start Galaxy, I get the following:
Traceback (most recent call last):
File "/galaxy-dev/lib/galaxy/web/buildapp.py", line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/galaxy-dev/lib/galaxy/app.py", line 71, in __init__
self.security = security.SecurityHelper( id_secret=self.config.id_secret )
File "/galaxy-dev/lib/galaxy/web/security/__init__.py", line 36, in __init__
self.id_cipher = Blowfish.new( self.id_secret )
ValueError: Maximum key size is 448 bits
I'm totally lost on this one. Does anyone have an idea or a hint on where to start? It would be highly appreciated!
Thanks a lot!
My apologies for reposting this, but I thought I ought have asked this in a
separate thread instead of appending it to a previous message. Anyway, I
was able to set up a folder for a user (in my case, my own non-admin user
account). universe_wsgi.ini's been configured to allow users to utilize a
data library. I've also created a library for my non-admin user account.
When all was set, I tried uploading a file to the library. But Galaxy
prompted me that the folder did not contain any valid files. I thought I
provided the wrong path; I even thought I really did not put anything in
the folder. But when I checked, every thing seemed fine. I'm really
stumped. I've searched the mailing list and even the wiki, and
unfortunately I was not able to find a decent answer. I changed the file
extension to .fastq and I indicated that the file to be uploaded was a
FASTQ one, as Jen has suggested. I still got the same error in the end.
I've scanned the universe_wsgi.ini file to see if there's anything else
that I needed to configure, but I found none.
Thanks in advance for your help!