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Error with functional tests on cluster
by Sandra Derozier 02 Sep '14

02 Sep '14

Hi all, I try to set up functional tests on different tools on my Galaxy portal. When I run functional tests locally everything works fine. But when I run them on the cluster it failed with this message : /bin/sh: module: line 1: syntax error: unexpected end of file /bin/sh: error importing function definition for `module' The execution on the cluster is ok but the dataset state is set to ERROR. The DIFF between the expected result and the obtained result is null. Indeed, this two files are the same. As I do not know what the problem is: do you have an idea? Thanks, Sandra DEROZIER

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testing the visualization plugins
by Hans-Rudolf Hotz 01 Sep '14

01 Sep '14

Hi As part of my upgrade/testing work, I am looking at the visualization plugins. In a new galaxy installation ("latest_2014.08.11"), they (ie 'Charts', 'Scatterplot', and 'Trackster') seem to work fine. All I have done was: - I defined the visualization_plugins_directory in the universe_wsgi.ini file If I comment-out this line, I only get trackster, when I click on the icon which looks like a bar-plot Next, I have tried it on our development server (after I have upgraded from "release_2014.04.14" to "latest_2014.08.11"). I changed the universe_wsgi.ini file. I the logs I get: galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,639 VisualizationsRegistry, loaded plugin: charts galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,641 VisualizationsRegistry, plugin load failed or disabled: ./config/plugins/visualizations/circster. Skipping... galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,655 VisualizationsRegistry, loaded plugin: graphview galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,657 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,675 VisualizationsRegistry, loaded plugin: scatterplot galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,677 VisualizationsRegistry, plugin load failed or disabled: ./config/plugins/visualizations/sweepster. Skipping... galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,679 VisualizationsRegistry, loaded plugin: trackster wrt to 'Charts', 'Scatterplot', and 'Trackster', this looks fine to me. However, if I hoover over the bar-plot icon, "Visualize in Trackster" pops up (instead of just "Visualize"), and when I click on it I get straight to the Trackster page, where, I am asked to define the Browser name and the Reference genome. No links for 'Charts' and 'Scatterplot'. On the other hand, the plug in infrastructure seems to work: If I change ~/config/plugins/visualizations/trackster/config/trackster.xml I see the effects, ie if I change result_type="datatype">data.Data< to result_type="datatype">interval.Interval I can restrict the visualization to only the interval data. Somehow, I am running a mixture of the 'old' and the 'new' visualization set-up ? Has anyone seen similar problems when testing the new plug in infrastructure on an old/upgraded Galaxy installation Thank you very much for any hints and help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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error with multi dataset tool run
by Robert Baertsch 01 Sep '14

01 Sep '14

I submitted 13 fastq files to tophat2 using DRMAA and got this error. Is it fatal? BTW: This is a super cool feature. I’m running the following version of galaxy-dist. changeset: 14212:91547729ffde branch: stable tag: tip user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Aug 29 14:00:23 2014 -0400 summary: Update tag latest_2014.08.11 for changeset ea12550fbc34 -Robert There were errors setting up 2 submitted job(s): Error executing tool: (OperationalError) database is locked u'UPDATE history_dataset_association SET update_time=?, name=?, blurb=? WHERE history_dataset_association.id = ?' ('2014-08-30 23:14:44.683957', 'Tophat2 on data 7: insertions', 'queued', 137) Error executing tool: (OperationalError) database is locked u'UPDATE dataset SET update_time=?, state=? WHERE dataset.id = ?' ('2014-08-30 23:15:57.204718', 'queued', 446)

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Problem Running TopHat2
by Kevin 30 Aug '14

30 Aug '14

Hello All, I am running a Galaxy instance on Linux and have installed tools from the Galaxy Main Tool Shed. However, whenever I run TopHat2, the program is unable to complete the job before I get the following error message: Traceback (most recent call last): File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found So far, I have made sure that the samtools do appear to be installed since they can be found listed under "Managed Installed Tool Shed Repositories". Is it possible that they were installed incorrectly? Any help is much appreciated. Thanks for taking the time to read this, Kevin Chang

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September 2014 Galaxy News
by Dave Clements 29 Aug '14

29 Aug '14

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Grouping of tools inside of toolbox does not work
by Björn Grüning 28 Aug '14

28 Aug '14

Hi, I have multiple version of the ncbi-blast+ wrapper installed. But they appear twice or a few of them even tripled in the toolbox. Expected behavior is only one tool in the toolbox and a select box inside of the tool. I have prepared a docker galaxy-blast container as test case. https://registry.hub.docker.com/u/bgruening/galaxy-blast/ https://github.com/bgruening/docker-recipes/tree/master/galaxy-blast Reproducible bugs with Docker! Cheers, Bjoern

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refresh_on_change : is this a valid attribute? Any other ideas/options??
by Lukasse, Pieter 27 Aug '14

27 Aug '14

Hi, I'm trying to get a wrapper from someone else working and I found this "refresh_on_change" attribute in his select boxes which are filled using the dynamic_options feature: <param name="col_type" type="select" label="Select column type" refresh_on_change="true" display="radio" dynamic_options='get_column_type(library_file)' help="" /> <param name="polarity" type="select" label="Select polarity" refresh_on_change="true" display="radio" dynamic_options='filter_column(library_file,col_type)' help="" /> ... When searching the documentation/wiki I do not find a reference to this, but it would be a nice option to have ;) Question: is there any way I can force a refresh when the user selects another option from such a select box. As you can see in the example above, this is needed because the next select box has its dynamic options built up by a function that takes the value from the previous select (col_type - highlighted above) as an input parameter. Currently this tool only works by showing each select in its own <page> , which is a deprecated option and prevents the tool from being used in a workflow... :( Thanks for your help! Best regards, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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Multiple output datasets
by Martin Christiansen 27 Aug '14

27 Aug '14

Hi all, I'm implementing a tool for our local galaxy instance which has multiple output datasets. The number of datasets are determined by the input so I've been following the instructions at the bottom of this page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files. As I understand, the $__new_file_path__ option is changed in the universe_wsgi.ini file. Regardless, the extra files created from the tool does not show in the galaxy history. Any ideas? Best, Martin Christiansen

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Re: [galaxy-dev] Cluster jobs running as real user
by Linda Cham 27 Aug '14

27 Aug '14

Follow the Galaxy wiki https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_… setup permission instructions. Follow these 2 steps to get Galaxy to run as real users with IBM Platform LSF: Step 1) Download the latest LSF DRMAA 1.1.1 from github. https://github.com/PlatformLSF/lsf-drmaa Level commit e4d5c1ab10fcba572eaede68fc2fc05332198bec or above This fixes the LSF job id not found issue. Step 2) LSF needs to disable message being printed out via the LSF environment variable "BSUB_QUIET". This can be done either in in Galaxy drmaa_external_runner.py file or in the galaxy admin environment profile Edit the drmaa_external_runner.py file to add in the LSF environment variable "BSUB_QUIET" to disable message print out. Line in blue below. scripts/drmaa_external_runner.py: def main(): userid, json_filename, assign_all_groups = validate_paramters() set_user(userid, assign_all_groups) json_file_exists(json_filename) os.environ['BSUB_QUIET'] = 'Y' s = drmaa.Session() s.initialize() jt = s.createJobTemplate() load_job_template_from_file(jt, json_filename) OR Disable LSF message in the galaxy admin profile e.g. export BSUB_QUIET=Y in .bash_profile Regards, Linda

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proxy / ssl
by Shrum, Donald C 26 Aug '14

26 Aug '14

Thanks for the help today Eric... I'm not sure if this is worth adding to the docs but I thought I'd post it in case someone would like to. I have an apache proxy setup for galaxy with ldap authentication. I wanted the user sign on to be over https as users are using their HPC accounts to sign in. I modified /etc/httpd/conf/httpd.conf to redirect requests from http to https: RewriteEngine On RewriteCond %{HTTPS} !=on RewriteRule ^/?(.*) https://%{SERVER_NAME}/$1 [R,L] I then added the proxy configuration to /etc/httpd/conf.d/ssl.conf to the virtual host section: <VirtualHost _default_:443> RewriteEngine On RewriteRule ^/static/style/(.*) /panfs/storage.local/opt/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /panfs/storage.local/opt/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /panfs/storage.local/opt/galaxy-dist/static/$1 [L] RewriteRule ^/favicon.ico /panfs/storage.local/opt/galaxy-dist/static/favicon.ico [L] RewriteRule ^/robots.txt /panfs/storage.local/opt/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://144.174.51.187:8080$1 [P]

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