Hello!
Im looking for a way to run jar files(or class files) as a tool.
Im not sure how to setup the galaxy instance to do this.
For some reason i am running into a classpath issue.
Anyone that could guide me in the right direction?
Regards
Frederick
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Edward Kirton wrote:
> Hi Nate, can I access the values in the universe_wsgi.ini file? How would I
> retrieve the value of "smtp_server" for example? (Or do i just parse the
> file myself?)
$__app__.config.smtp_server should do it. Most variables should match
the name in the config file - a few
Hello Olivier,
The first place to start is to change the metadata for the history items
so that the filetype is .fastq. Do this by clicking on the pencil icon
for each dataset, change the filetype, and save. Or, rename the files
before transfer.
If there are still problems, double check the
Hi Nate, can I access the values in the universe_wsgi.ini file? How would I
retrieve the value of "smtp_server" for example? (Or do i just parse the
file myself?)
Thanks!
On Fri, May 6, 2011 at 9:06 AM, Nate Coraor wrote:
> __tool_data_path__ = GALAXY_DATA_INDEX_DIR = universe_wsgi.ini
>to
I need to be able to set some metadata in some custom data types. For now, I'm
just trying to set the value of the 'misc_info' field. The client script is
this:
put( sys.argv[1], sys.argv[2], { 'update_type' : 'metadata', 'misc_info' :
'meta data msg' } )
and my API method is as follows. It exec
Hello Leandro,
On the main Galaxy site, an automatic email function is not currently
possible (but the suggestion is a good one!). If you are running your
own instance, this is something that could likely be written up and
added in (and shared with other user's through the tool shed).
For se
Duddy, John wrote:
> So, to summarize:
> 1 - I can upload files via the API now, which returns the id
> 2 - If I don't upload via directory paths, the file upload will not be
> instant, so I'll have to use a poller to find out when the file upload is done
> 3 - I can write a new API to set metadat
So, to summarize:
1 - I can upload files via the API now, which returns the id
2 - If I don't upload via directory paths, the file upload will not be instant,
so I'll have to use a poller to find out when the file upload is done
3 - I can write a new API to set metadata on a dataset and call that
Hi Nate,
thanks for answering. I performed some tests "stealing" PCs from my
collegues and actually it was a problem of my profile data. I experienced
these problems with both Chromium and Firefox on my machine, but with others
it works, so I decided to simply clean up my profile data and now it wo
Marina Gourtovaia wrote:
> Line 298 of galaxy-dist/tool_conf.xml in the zipped distribution
> downloaded yesterday
>
> "
>
> should be
>
>
>
> ?
Hi Marina,
Indeed, thanks for catching this. It has been fixed and will go out in
the next stable release (probably next week).
--nate
>
> Mari
Peter Cock wrote:
> On Fri, May 6, 2011 at 8:18 AM, Hans-Rudolf Hotz wrote:
> > Hi Ed
> >
> > You can use the variable "$userEmail" in the 'command' tag of the tool
> > definition file
> >
> > Regards, Hans
>
> That should probably be listed on the wiki,
> https://bitbucket.org/galaxy/galaxy-cent
Duddy, John wrote:
> I'm looking at extending the metadata fields for one of the supported file
> types. The files can get VERY large, and since I'm creating those files, I'd
> like to save as metadata some of the information I have on the contents.
>
> Specifically, I'd like to tag the files wi
Liisa Koski wrote:
> Hi,
> Yesterday I ran the cleanup_datasets.py scripts as follows..
>
> Deleting Userless Histories
> python cleanup_datasets.py universe_wsgi.ini -d 10 -1
>
> Purging Deleted Histories
> python cleanup_datasets.py universe_wsgi.ini -d 10 -2 -r
>
> Purging Deleted Datasets
>
Marco Moretto wrote:
> Hi all,
> I successfully installed a Galaxy instance locally. I use Galaxy with
> Apache. Every time I try to download a file from history (like Options ->
> Export to file) the browser (Firefox 3.6) reply with the error
> "/tmp/lFeL6erm.asc.part could not be saved, because t
Vipin TS wrote:
> Dear Galaxy Team,
>
> I am switching our Galaxy production service to a new machine, We are using
> Postgres as database server.
> The existing database belongs to postgres version 8.3 and I took my
> instance's dump using postgres version 8.4.
> I am able to restore my database
Line 298 of galaxy-dist/tool_conf.xml in the zipped distribution
downloaded yesterday
"
should be
?
Marina
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2
Hi
Hi
I currently use a galaxy server with cluster. This cluster uses SGE.
I'd like to specify a queue other than the default.
I have tried many combinaisons with drmaa:/// without success. The
queue used is always the default one.
I've just configured my Galaxy instance to work to submit to
On Fri, May 6, 2011 at 10:17 AM, SHAUN WEBB wrote:
>
> Hi, I have created a tool that will fetch sequences for selected IDs from a
> tabular file containing multiple IDs and additional info.
>
> I want the tool config to scan the first column of the tab file for IDs and
> provide the user with a s
Hi, I have created a tool that will fetch sequences for selected IDs
from a tabular file containing multiple IDs and additional info.
I want the tool config to scan the first column of the tab file for
IDs and provide the user with a selection box where they can select a
single ID or mult
On Fri, May 6, 2011 at 8:18 AM, Hans-Rudolf Hotz wrote:
> Hi Ed
>
> You can use the variable "$userEmail" in the 'command' tag of the tool
> definition file
>
> Regards, Hans
That should probably be listed on the wiki,
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
Are there a
Hi Darren
I assume, you have created a new data type
https://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes
You can now disable the 'sniffing' by adding the data type to the
following line:
unsniffable_binary_formats = [ 'ab1', 'scf' ]
in:
~/galaxy-dist/lib/galaxy/datatypes/bina
Hi
In your_galaxy_root_path/lib/galaxy/datatypes/binary.py try adding the
extension of your suffix array file type in the
unsniffable_binary_formats array.
It would be a good idea to add a class for this file type here too and
make sure the datatypes_conf.xml file refers to it.
Hope that h
Hi Ed
You can use the variable "$userEmail" in the 'command' tag of the tool
definition file
Regards, Hans
On 05/06/2011 03:56 AM, Edward Kirton wrote:
is there a variable i can use in the tool config xml file?
thanks!
ed
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