Any chance you have cleanup_job=never in universe_wsgi.ini? I recently
pushed a bugfix to galaxy-central - history import wouldn't work if
that is set.

Otherwise you may want to review this thread for clues:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-December/017773.html

-John

On Thu, Feb 6, 2014 at 10:34 AM, graham etherington (TSL)
<graham.ethering...@sainsbury-laboratory.ac.uk> wrote:
> Hi John,
> Thanks for your suggestion. I included the suggested line in my job_conf.xml
> file and sure enough the job was run locally. It exits without any errors,
> but unfortunately it still didn't work - the imported history doesn't appear
> in the history panel. Here's the output from the paster log...
>
> galaxy.jobs DEBUG 2014-02-06 14:48:38,463 (714) Working directory for job
> is:
> /tsl/services/galaxy/dist/galaxy-dist/database/job_working_directory/000/714
> galaxy.jobs.handler DEBUG 2014-02-06 14:48:38,471 (714) Dispatching to local
> runner
> galaxy.jobs DEBUG 2014-02-06 14:48:38,544 (714) Persisting job destination
> (destination id: local)
> galaxy.jobs.handler INFO 2014-02-06 14:48:38,595 (714) Job dispatched
> galaxy.jobs.runners.local DEBUG 2014-02-06 14:48:38,854 (714) executing:
> export GALAXY_SLOTS="1"; python
> /tsl/services/galaxy/dist/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
> http://galaxy.tsl.ac.uk/u/ethering/h/galaxy-intro
> /tsl/services/galaxy/dist/galaxy-dist/database/tmp/tmp4yCMyk --url
> galaxy.jobs DEBUG 2014-02-06 14:48:38,936 (714) Persisting job destination
> (destination id: local)
> galaxy.jobs.runners.local DEBUG 2014-02-06 14:48:45,024 execution finished:
> export GALAXY_SLOTS="1"; python
> /tsl/services/galaxy/dist/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
> http://galaxy.tsl.ac.uk/u/ethering/h/galaxy-intro
> /tsl/services/galaxy/dist/galaxy-dist/database/tmp/tmp4yCMyk --url
> galaxy.jobs DEBUG 2014-02-06 14:48:45,179 job 714 ended
>
> ...and here's a skimmed down version of my job_conf.xml file (TSL-Test128 is
> the default LSF queue that Galaxy jobs are sent to)
>
> <?xml version="1.0"?>
> <job_conf>
>     <plugins workers="8">
>         <plugin id="local" type="runner"
> load="galaxy.jobs.runners.local:LocalJobRunner" workers="16"/>
>         <plugin id="drmaa" type="runner"
> load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="8"/>
>     </plugins>
>     <handlers default="handlerLocal">
>         <handler id="main" tags="handlerLocal"/>
>     </handlers>
>     <destinations default="TSL-Test128">
>         <destination id="local" runner="local"/>
>         <destination id="TSL-Test128" runner="drmaa" tags="LSF,Test128">
>     </destination>
>     </destinations>
>     <tools default="local">
>         <!--make the import histories tool run locally-->
>         <tool id="__IMPORT_HISTORY__" destination="local"/>
>     </tools>
> </job_conf>
>
> I'm presuming if there was something wrong with the xml that an error would
> be thrown, so I'm not sure if there's something else that I'm missing.
> Many thanks,
> Graham
>
>
>
> From: John Chilton <chil...@msi.umn.edu>
> Date: Thursday, 6 February 2014 14:32
> To: "graham etherington (TSL)"
> <graham.ethering...@sainsbury-laboratory.ac.uk>
> Cc: Galaxy Dev <galaxy-dev@lists.bx.psu.edu>
> Subject: Re: [galaxy-dev] Running Import History from File as local job
>
> Hello Dr. Etherington,
>
> The id of the special tool is __IMPORT_HISTORY__ so if you have a
> local destination called local, the following tool entry SHOULD force
> local import - seemed to function the way I expected in a quick test
> anyway:
>
> <tool id="__IMPORT_HISTORY__" destination="local"  />
>
> Hope this helps,
> -John
>
> On Thu, Feb 6, 2014 at 6:12 AM, graham etherington (TSL)
> <graham.ethering...@sainsbury-laboratory.ac.uk> wrote:
>
> Hi,
> I have two local instances of Galaxy running (both entirely independent of
> each other and running on separate clusters). I'm trying to export a history
> from Instance A to Instance B, but so far have not been able.
> I've attempted this in two ways.
>
> 1. Download the Galaxy_history.tar.gz file from Instance A (Options > Export
> to File) and place it in a path on the filesystem which Galaxy B can see.
> Then Options >  Import from File and in the 'Archived History URL:' field
> place: '/full/path/to/Galaxy_history.tar.gz' (I've also tried
> 'file:///full/path/to/Galaxy_history.tar.gz')
> The job runs (submitted to LSF cluster) with no errors in paster.log, but
> the stdout file in the job_working_directory gives the error
> Exception getting file from URL: unknown url
> type:/full/path/to/Galaxy_history.tar.gz <open file '<stderr>', mode 'w' at
> 0x2ba2d4e9b1e0>
> Error unpacking tar/gz archive: nothing to open <open file '<stderr>', mode
> 'w' at 0x2ba2d4e9b1e0>
>
> 2.  Copy the url link for the History in Instance A (Options > Share or
> Publish ), then in Instance B go Options >  Import from File and in the
> 'Archived History URL:' field place the url provided by Instance A.
> Again the job runs OK, but the stdout file has the error:
> Exception getting file from URL: <urlopen error [Errno 111] Connection
> refused> <open file '<stderr>', mode 'w' at 0x2b359790a1e0>
> Error unpacking tar/gz archive: nothing to open <open file '<stderr>', mode
> 'w' at 0x2b359790a1e0>
>
> I'm pretty sure method number 2 is failing because the Import History job is
> being run on the cluster which cannot see the outside world (and hence
> Instance A). I think I should be able to overcome this by specifying in
> job_conf.xml that the import tool be run locally. The problem is, that I've
> not been able to identify what the actual tool or process is that runs the
> Import Histories method. I know that it produces a bash script which runs
> lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py, but not being a standard
> tool (i.e. found in the ./tools/ directory with an xml wrapper), I can't
> find an ID for it.
> Naively I tried the following in job_conf.xml: (I have 'local' defined in
> 'destinations' and 'plugins')
>
> <tools default="local">
>      <!--make the import histories tool run locally-->
>      <tool id="lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py"
> destination="local"/>
> </tools>
>
> But this made no difference.
>
> Does anyone know how I can either get the Import History tool to run locally
> or suggest another way to import my history?
>
> Many thanks,
> Graham
>
>
> Dr. Graham Etherington
> Bioinformatics Support Officer,
> The Sainsbury Laboratory,
> Norwich Research Park,
> Norwich NR4 7UH.
> UK
> Tel: +44 (0)1603 450601
>
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