I recently updated my local testing Galaxy install to the latest stable
version. When I went to test the working of HTML output in some scripts
that worked in previous installs of Galaxy, the latest stable version gave
me an empty return with a message of 'no peek' rather than outputting the
HTML output from previous runs of the same tool no longer shows the
but still works fine from the HTML file opened out of the file directory.
Any assistance on this issue would be greatly appreciated.
Bioengineering Major, George Mason University
Metabiome Informatics Group, Environmental Biocomplexity
We are running the latest stable distribution on our server. We want
tophat2 (along with other tools) to be executed on another machine.
LWR is setup based on the online documentation (
Bowtie2 is working as should but it looks like LWR is unable to return the
outputs from tophat2.
In universe_wsgi.ini the runner is configured like this:
bowtie2 = lwr://https://uniquestring@chaos:8913
tophat2 = lwr://https://uniquestring@chaos:8913
When running tophat2 the following error message is returned.
Traceback (most recent call last):
line 135, in finish_job
line 146, in download_work_dir_output
self.__raw_download_output(name, self.job_id, "work_dir", output)
line 174, in __raw_download_output
line 52, in __raw_execute
response = self.transport.execute(url, data=data,
line 21, in execute
response = self._url_open(request, data)
line 12, in _url_open
return urllib2.urlopen(request, data)
File "/usr/lib/python2.7/urllib2.py", line 127, in urlopen
return _opener.open(url, data, timeout)
File "/usr/lib/python2.7/urllib2.py", line 407, in open
response = meth(req, response)
File "/usr/lib/python2.7/urllib2.py", line 520, in http_response
'http', request, response, code, msg, hdrs)
File "/usr/lib/python2.7/urllib2.py", line 445, in error
File "/usr/lib/python2.7/urllib2.py", line 379, in _call_chain
result = func(*args)
File "/usr/lib/python2.7/urllib2.py", line 528, in http_error_default
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
We tried to specify tophat's output folder either directly in lwr's working
or output directory without success.
Is there a solution to this?
This is not a big issue but I am curious to know about it:
To have Trackster visualization working properly in Galaxy, one needs
Yet in our instance (running under Ubuntu OS), installing bedtools in the
galaxy home directory and setting the environmental variable PATH in the
.profile file so that it includes the path to ~/bin/bedtools does not work.
Yet the PATH variable is indeed including the appropriate information as
the owner of the galaxy home directory can run the bedtools in command
I have also to precise that we use a lot of third party tools (bowtie,
cufflinks, etc...) including wigToBigWig which is also required for
trackster, and that we have no path problem with these tools.
Indeed the only way to get galaxy accessing properly to the bedtools
currently is to put the bedtools in the /usr/local/bin directory. Here it
I suspect it is a problem of shell specification when the bedtools are used
for trackster, but I could not figure out further the issue.
Drosophila Genetics and Epigenetics
Laboratoire de Biolologie du Développement
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05
Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50
Hi, I am wondering how the nglims "Manage sequencers and external
services" works. I want to add our MiSeq such that all future runs show up
in Galaxy as data sets. Is this the way to do it?
When I use this menu to add our sequencer it asks for a username, ip
address, password, etc. I am not sure what it is really asking for
actually. All of the data from the MiSeq shows up on the same computer as
Galaxy, and so I am sure that I do not need an IP address except for
Is there any beginning documentation on this part of nglims? Or a tutorial
on how to detect new data and import it? Thanks.
Lee Katz, Ph.D.
One of our users is running the eXpress package under NGS: RNA
Analysis -> eXpress -- galaxy/dist/tools/ngs_rna/express_wrapper.*
I noticed the syntax for express_wrapper.xml has the following:
any reason why it was set to that, as opposed to:
In our setup, we need to source the env.sh file for express to setup
the correct environmental variables. Changing from binary to package
has not solved this and re-running the job never sources our env.sh
What am I doing wrong?
My tool dependency directory looks like so:
|---default --> 1.3.0
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
University of California, Irvine
I am getting the error "FATAL: sorry, too many clients already" in in my local Galaxy instance in the POSTGRES database log.
I have set max_connections = 1000 in already in "postgresql.conf" and STILL get this error...
I was running a Flowcell with about 96 samples and a workflow with about 50 steps each, but I never had a problem before when max_connections was set to 100 and did not change the database...
I do have a cluster that is much faster so i guess there may be several connections going to the database, but maybe there is some leakage in the galaxy code that is not closing the connections?
It really screws up the galaxy instance and jobs are just in limbo and never finsihed (in the database)...
database_engine_option_pool_size = 20
database_engine_option_max_overflow = 40
already but maybe I set those too high?
What is a normal setting for max_connections in galaxy production servers?
We are running a local Galaxy instance up-to-date against galaxy/galaxy-dist.
When we edit attributes of a dataset in current history and request a datatype change (Datatype tab), the selected dataset appears as a running job (yellow box with spinning icon) for ever. The type has been changed and if we refresh the history manually, the dataset appears in green again.
Is anyone experiencing the same issue ?
Directeur des systèmes d'information
Email : julien.seiler(a)igbmc.fr
Tel : 03 88 65 33 63
At UPPMAX, are interested both in Galaxy, and the GenomeSpace
project, and wanted to check if there are people on the Galaxy team
or other "galaxers" who are involved in the GenomeSpace project, that
will be in Oslo next week?
If so, I would be interested to meet up!
Developer at SNIC-UPPMAX www.uppmax.uu.se
Developer at Dept of Pharm Biosciences www.farmbio.uu.se
i have installed local instance of galaxy in my linux system.
i want to add an extra authentication mechanism before saving user information into database ....in which file i have to do modification .?