- galaxy-dev - lists.galaxyproject.org

Strange Issue with Data Library
by Patel, Viren 01 Jul '13

01 Jul '13

Hello. After creating a data library and clicking on the 'Manage Data Libraries' menu to show the list of libraries, clicking on a data library name results in an "Unable to connect" message in Firefox, no action in Safari, and an "Error 102 (net::ERR_CONNECTION_REFUSED): The server refused the connection." when using Chrome. However, in all browsers, copying the link and pasting it into a new window works fine (the datasets/folders of the library are displayed and I can work with them normally). There are no messages in the Galaxy logs, web server logs, or system logs. Any insights to resolve this? Thanks. ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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fastQ groomer waiting to run problem
by Xu, Ye 01 Jul '13

01 Jul '13

Hi there, I am using Galaxy at BioCloud Central. I have successfully transferred total 30GB fastQ data from amazon S3 to galaxy. I tried to run fastQ groomer for each samples. But it said the job is waiting to run. I have waited a couple days and the job is still waiting. I called AWS, they told me my cluster working fine. So I don't know why the job can't start. Thank you so much. Best, Ye Xu The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Patch in reference to trello card#968
by Eric Enns 01 Jul '13

01 Jul '13

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Re: [galaxy-dev] June update breaks saved histories
by Shane Sturrock 01 Jul '13

01 Jul '13

While I never got a reply to this, I did continue trying to figure it out and ended up doing a fresh install on our system and there histories worked. After a bit of back and forth with upgrading the previous install and database the issue appears to be with subtle changes to the universe_wsgi.ini file and starting with a fresh one that came with the new distribution, and then modifying that to suit our environment resulted in an upgrade where histories worked. Shane On 27/06/2013, at 4:00 AM, galaxy-dev(a)lists.bx.psu.edu wrote: > > I've tried updating a couple of times to the latest stable release and each time I find that I can no longer see my saved histories. Roll back my machine to an earlier snapshot and it is fine. The thing that may be different about our system is that we're using Apache authentication rather than using the built in accounts. Nothing about the apache install has changed, just do the update to the June release, start it, run the manage_db.sh upgrade and restart (database is on postgres by the way) and then saved histories is empty and creating new histories never populates the list either. I would like to upgrade since the previous release had issues with sending BAM files to UCSC which this update has fixed. > > Maybe it's related to the upgraded SQLAlchemy? > > Shane -- For urgent cases, contact support(a)biomatters.com Dr Shane Sturrock shane.sturrock(a)biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand

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(no subject)
by Dave Clements 30 Jun '13

30 Jun '13

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Empty & 'no peek' Returned Instead of HTML Output?
by Amanda Zuzolo 29 Jun '13

29 Jun '13

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 file with the embedded Javascript functionality. Additionally, the HTML output from previous runs of the same tool no longer shows the Javascript file/functionality when opened from the eye button in Galaxy, but still works fine from the HTML file opened out of the file directory. Any assistance on this issue would be greatly appreciated. -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity

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Tophat2 output issue on LWR runner
by Nikos Sidiropoulos 28 Jun '13

28 Jun '13

Hi 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 ( http://wiki.galaxyproject.org/Admin/Config/LWR, https://lwr.readthedocs.org/en/latest/) 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: [galaxy:tool_runners] 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): File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 135, in finish_job client.download_work_dir_output(source_file, job_wrapper.working_directory, output_file) File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py", line 146, in download_work_dir_output self.__raw_download_output(name, self.job_id, "work_dir", output) File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py", line 174, in __raw_download_output output_path=output_path) File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py", line 52, in __raw_execute response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py", line 21, in execute response = self._url_open(request, data) File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py", 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 return self._call_chain(*args) 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? Bests, Nikos

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Path to the bedtools for getting trackster working properly
by Christophe Antoniewski 28 Jun '13

28 Jun '13

Hi everybody, This is not a big issue but I am curious to know about it: To have Trackster visualization working properly in Galaxy, one needs bedtools. 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 lines. 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 works ! 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. Cheers Christophe -- Christophe Antoniewski 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 http://drosophile.org

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Managing a sequencer
by Lee Katz 28 Jun '13

28 Jun '13

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 localhost. 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.

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Tool Dependency Check for eXpress - requirements syntax incorrect?
by Adam Brenner 27 Jun '13

27 Jun '13

Howdy, 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: <requirement type="binary">eXpress</requirement> any reason why it was set to that, as opposed to: <requirement type="package">eXpress</requirement> 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 file. What am I doing wrong? My tool dependency directory looks like so: galaxy/dist/tool_dependency/eXpress/ |---default --> 1.3.0 |----1.3.0/env.sh Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne(a)uci.edu

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