> yes, I was the only user but I guess it is too fragile for this kind of thing. postgres wasn’t queuing age jobs correctly so I guess I should track down why.
> > From: Hans-Rudolf Hotz <h...@fmi.ch> > Subject: Re: [galaxy-dev] error with multi dataset tool run > Date: September 1, 2014 at 5:54:10 AM PDT > To: Robert Baertsch <baert...@soe.ucsc.edu>, <galaxy-dev@lists.bx.psu.edu> > > > Hi Robert > > Are you using the built in SQLite database ? > > Hans-Rudolf > > On 08/31/2014 01:27 AM, Robert Baertsch wrote: >> 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 <n...@bx.psu.edu <mailto:n...@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)* >> >> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > > > > From: Sandra Derozier <sandra.deroz...@jouy.inra.fr> > Subject: [galaxy-dev] Error with functional tests on cluster > Date: September 1, 2014 at 6:54:41 AM PDT > To: galaxy-...@bx.psu.edu > > > 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 > > Sandra DEROZIER > Unité Mathèmatique, Informatique et Génome (MIG) > Plateforme MIGALE > Bâtiment 233 > Domaine de Vilvert > 78352 Jouy-en-Josas Cedex > > > > From: Hans-Rudolf Hotz <h...@fmi.ch> > Subject: [galaxy-dev] Solved - Re: testing the visualization plugins > Date: September 1, 2014 at 8:13:30 AM PDT > To: "<galaxy-...@bx.psu.edu>" <galaxy-...@bx.psu.edu> > > > Hi all > > First of all, a big Thanks to Carl who helped me fixing this problem. > > So as a summary for all, the problem was caused by a datatype (an extension > to tabular), I manually added to "datatypes_conf.xml" > > Removing the datatype fixed the problem. I couldn't identify a syntax > problem, neither in "datatypes_conf.xml" nor in > "~/lib/galaxy/datatypes/registry.py" and "~/lib/galaxy/datatypes/tabular.py". > However, renaming it (in all three files) fixed it as well. > > Regards, Hans-Rudolf > > > > _______________________________________________ > galaxy-dev mailing list > galaxy-dev@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
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