galaxy-dev June 2013

galaxy-dev@lists.galaxyproject.org

111 participants
189 discussions

(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

2 1

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

2 3

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

2 2

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.

1 0

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

2 2

Getting "FATAL: sorry, too many clients already" in postgres database
by Anthonius deBoer 27 Jun '13

27 Jun '13

Hi, 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)... Any ideas? I adjusted 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? Thanks, Thon

1 0

Dataset appears as running job in history when changing datatype
by Julien SEILER 27 Jun '13

27 Jun '13

Dear all, 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 ? Regards, Julien -- Julien Seiler IGBMC Directeur des systèmes d'information Email : julien.seiler(a)igbmc.fr Tel : 03 88 65 33 63

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Any Galaxers working on GenomeSpace, going to Oslo?
by Samuel Lampa 27 Jun '13

27 Jun '13

Hi, At UPPMAX, are interested both in Galaxy, and the GenomeSpace project[1], 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! BestRegards // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se

1 0

Extra authentication
by shashi shekhar 27 Jun '13

27 Jun '13

Hi, 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 .? regards shashi

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galaxy-dev June 2013