Question Regarding Local Galaxy Installation Uploading Files Error
by George Yianni Michopoulos
To any wonderful person that can help me:
I recently uploaded a local instance of Galaxy on a new computer at the Fernald Lab at Stanford. I am not too familiar with Unix, but needed to install the local instance due to the high volume of genomic data we will be processing, and so that we could install/use the FastX toolkit. I managed to successfully install the toolkit, but now I just realized that I can't seem to upload any of my correctly formatted data files. The error I get is pasted below:
"Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_4; en-us) AppleWebKit/533.18.1 (KHTML, like Gecko) Version/5.0.2 Safari/533.18.5"
Debug at: http://localhost:8080/_debug/view/1303859435
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 61553)
Traceback (most recent call last):
File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread
self.finish_request(request, client_address)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 617, in __init__
self.handle()
File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in handle
BaseHTTPRequestHandler.handle(self)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServer.py", line 329, in handle
self.handle_one_request()
File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in handle_one_request
self.wsgi_execute()
File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 287, in wsgi_execute
self.wsgi_start_response)
File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/urlmap.py", line 202, in __call__
return app(environ, start_response)
File "/Users/***/bin/fastx_bin/galaxy_test/lib/galaxy/web/framework/middleware/xforwardedhost.py", line 21, in __call__
return self.app( environ, start_response )
File "/Users/***/bin/fastx_bin/galaxy_test/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/config.py", line 164, in __call__
app_iter = self.application(environ, start_response)
File "/Users/***/bin/fastx_bin/galaxy_test/lib/galaxy/web/framework/middleware/translogger.py", line 68, in __call__
return self.application(environ, replacement_start_response)
File "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 226, in __call__
return self.respond(environ, start_response)
File "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 399, in respond
if self.xmlhttp_key in req.params:
File "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 900, in params
params = self.str_params
File "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 892, in str_params
return NestedMultiDict(self.str_GET, self.str_POST)
File "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 818, in str_POST
keep_blank_values=True)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 508, in __init__
self.read_multi(environ, keep_blank_values, strict_parsing)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 632, in read_multi
environ, keep_blank_values, strict_parsing)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 510, in __init__
self.read_single()
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 647, in read_single
self.read_lines()
File "/Users/***/bin/fastx_bin/galaxy_test/lib/galaxy/web/framework/base.py", line 253, in read_lines
self.read_lines_to_outerboundary()
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 697, in read_lines_to_outerboundary
line = self.fp.readline(1<<16)
File "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 467, in readline
data = self.file.readline(self.length - self._consumed)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/socket.py", line 409, in readline
bline = buf.readline(size)
OverflowError: long int too large to convert to int"
(I replaced irrelevant components of the file path with *** for confidentiality purposes)
Do you have any idea what the problem is and how I can fix it? I feel like it has something to do with my python, but I downloaded 2.6.6, which I thought should work according to the Install Readme. Thanks so much for your help!
Sincerely,
George Michopoulos
Stanford University '13
on behalf of the Fernald Lab
10 years, 9 months
tool parameter attribute for option display value (not passed value)?
by Leandro Hermida
Hi,
For a tool select input parameter:
<param name="input1" type="select">
<option value="hs33">Homo sapiens</option>
<option value="mm19">Mus musculus</option>
<option value="rn43">Rattus norvegicus</option>
</param>
Is there an attribute for the variable $input1 that will give me the
displayed value (e.g. Homo sapiens, not hs33)?
thank you,
Leandro
10 years, 9 months
Link address to specific section of tools in Galaxy
by Vipin TS
Dear Galaxy Team,
Any idea how I can access a specific section of tools from a Galaxy instance
?
For example:
In our Galaxy instance at http://galaxy.tuebingen.mpg.de/, we have a section
called 'Gene Finding'.
Under this we have several sub sections and I would like to invoke a
specific sub section let's say
mGene.web through a link address. In Galaxy I know we can specifically call
a tool page through
the link address. My concern is that if I call for the sub section, is there
any chance to load the first
tool from that section to the tool page and list the available tools in tool
panel frame.
Many thanks for your great effort.
Vipin
Friedrich Miescher Laboratory
of the Max Planck Society
Spemannstrasse 39, 72076
Tuebingen, Germany
10 years, 9 months
problem running latest "galaxy-central"
by Assaf Gordon
Question:
The recent galaxy-central revision ( 2b057869b72f ) doesn't work on my computer, saying "DistributionNotFound: cython>=0.12.1".
Example:
$ hg clone http://bitbucket.org/galaxy/galaxy-central/ galaxy_hidden_dataset_test
$ cd galaxy_hidden_dataset_test
$ hg id
2b057869b72f tip
$ sh run.sh
...
...
...
Traceback (most recent call last):
File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/web/buildapp.py", line 81, in app_factory
from galaxy.app import UniverseApplication
File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/app.py", line 11, in <module>
from galaxy.tools.imp_exp import load_history_imp_exp_tools
File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module>
from galaxy.web.base.controller import UsesHistory
File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/web/base/controller.py", line 12, in <module>
from galaxy.visualization.tracks.data_providers import get_data_provider
File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/visualization/tracks/data_providers.py", line 11, in <module>
pkg_resources.require( "pysam" )
File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py", line 404, in require
return c[req.project_name].require()
File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py", line 237, in require
dists = self.resolve()
File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py", line 195, in resolve
return self.version_conflict( e.args[0], e.args[1] )
File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py", line 226, in version_conflict
r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch )
File "/home/gordon/temp/galaxy_hidden_dataset_test/lib/pkg_resources.py", line 565, in resolve
raise DistributionNotFound(req) # XXX put more info here
DistributionNotFound: cython>=0.12.1
=============
I'm running debian/stable, with Python 2.6.6 (r266:84292, Dec 26 2010, 22:31:48)
Do I need to install something (cython) ?
-gordon
10 years, 9 months
User Name "not set" with external LDAP authentication
by Leandro Hermida
Hi,
Just wondering if I got my setup right, I have Galaxy front-ended by Apache
doing the static caching, proxying and LDAP auth. What's nice is that
user's don't have to be created by an admin if the user authenticates and
authorizes properly against the LDAP config then Galaxy will automatically
create the user locally.
My question is that it shows that the User Name is "not set" for such users,
is this the way its supposed to be or can I modify my LDAP config in such a
way that it does set a User Name?
regards,
Leandro
10 years, 9 months
Getting tool dirpath in a Python code file
by Leandro Hermida
Hi,
I have a tool with a <code file="my_script.py"/> tag and in that code file
I'm trying to get the tool dirpath where that script and the tool XML
exist. I've tried:
os.path.abspath(os.path.dirname(sys.argv[0]))
os.path.abspath(os.path.dirname(__file__))
And both don't work as expected. Is there a galaxy class I could import
which will have the tool directory path?
regards,
Leandro
10 years, 9 months
Huge Output Files in Galaxy (in compute cluster)
by Marc Bras
Hi All,
I use Galaxy on a compute cluster and each job is launch in a node.
When I launch a workflow and when it generates very huge files (some
Go), the job finish (I can see that with 'qstat' command) but Galaxy
takes several minutes (or some hours !!) to display a green Box in history.
It seems running... but it's already finished in the cluster !!
I think Galaxy is checking the output file...
Is it normal ?
Is it possible to skip this check ?
Thanks in advance,
Marc
--
Marc Bras
------------------------------------------
Marc.Bras(a)versailles.inra.fr
INRA-URGI:
Unité de Recherche Génomique Info
Centre de Recherche de Versailles-Grignon
Route de Saint Cyr
78026 Versailles - FRANCE
Tel: +33 1 30 83 34 70
------------------------------------------
10 years, 9 months
Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?
by Whyte, Jeffrey
Hi Everyone,
I'm having trouble getting some of the tools to work on my local installation of Galaxy on a Mac (OS X version 10.6.7). The instructions on the GetGalaxy wiki are clear, and I was able to download and install from the anonymous Mercurial repository. Galaxy starts up and runs just fine for tools like "Get Data", "FASTQ Groomer", and "FASTQ Summary Statistics".
The problems started when I try to run Graph/Data Display -> Boxplot (GnuPlot). I get the error:
"An error occurred running this job:/bin/sh: gnuplot: command not found
Error running gnuplot."
The FASTX Barcode Splitter also gives me an error:
"An error occurred running this job:/Users/Me/galaxy-dist/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh: line 65: fastx_barcode_splitter.pl: command not found
zcat: /Users/Me/galaxy-dist/database/files/000/dataset_10.dat.Z: No such file or directory
sed: illegal opt"
I'm assuming these are Tool Dependency problems, although I have tried to install the OS X versions of GnuPlot and the FASTX Toolkit and still get errors.
Are there any suggestions from users who are successfully running Galaxy on OS X?
Thanks in advance,
Jeff
10 years, 9 months
