that is set.
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
/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
/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
Date: Thursday, 6 February 2014 14:32
To: "graham etherington (TSL)"
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)
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
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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