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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