September 2014 - galaxy-dev - lists.galaxyproject.org

Proposal: Create a public archive of the GalaxyProject IRC Channel
by Dave Clements 02 Sep '14

02 Sep '14

Hello all, We would like to change the logging policy for the #galaxyproject IRC channel <https://wiki.galaxyproject.org/GetInvolved#IRC_Channel>: - *Starting later this fall, the #galaxyproject IRC channel <https://wiki.galaxyproject.org/GetInvolved#IRC_Channel> will be logged online in a format that can be searched.* Currently, this channel is not logged anywhere. This change will only be made if the community agrees that a searchable online log would be an improvement. *If you have thoughts or comments on this proposal, then please post them to this Biostar thread <http://bit.ly/gxybs8804>*. In two weeks' time (around September 17, 2014), we'll summarize the discussion and publish a decision. *Proposal Details:* Starting sometime after community discussion ends (and assuming that discussion is favorable): 1. At least two weeks before the change: 1. Warnings will be added to the IRC channel information and on the wiki, that the log will be publicly archived as of the given start date. 2. The policy change will be announced on Galaxy Biostar <https://wiki.galaxyproject.org/Support/Biostar> and the Galaxy-Dev and Galaxy-Announce mailing lists <https://wiki.galaxyproject.org/MailingLists>. 2. On the launch date 1. The IRC channel (and the wiki) will be updated to clearly state that the IRC channel is publicly logged. 2. Announcements of the change will be posted to Biostar and the mailing lists. 3. IRC postings from the announcement onward will start showing up in the public log. 4. The IRC channel log will be included in the Galaxy search engines <http://galaxyproject.org/search/>. *Why now?* The project's IRC channel came up at the GalaxyAdmins BoF meetup <https://wiki.galaxyproject.org/Events/GCC2014/BoFs/GalaxyAdmins> at GCC2014 <https://wiki.galaxyproject.org/Events/GCC2014>, where it was lauded as both a great resource, *and cursed because it is not archived anywhere.* An action item from that meetup is to propose this change. The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Retrieving json files
by Saket Choudhary 02 Sep '14

02 Sep '14

Is there a way to retrieve fileX.json in history using the DataProviders? Using https://wiki.galaxyproject.org/DataProviders I tried "base" and "line", but I am looking for retrieving the contents of fileX.json as a json object itself. Saket

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API for multi-file upload
by Neil.Burdett＠csiro.au 02 Sep '14

02 Sep '14

Hi, I really like the multi-file upload tool in the latest version of Galaxy. Is there an API for it so we can send files via a script rather than using the user interface? If so are there any examples? Thanks Neil

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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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