Re: [galaxy-dev] quick question: how can i supply the user's email address to a tool?

2011-05-06 Thread Hans-Rudolf Hotz
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 ___

Re: [galaxy-dev] Uploading Binary Files into Galaxy

2011-05-06 Thread Louise-Amelie Schmitt
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

Re: [galaxy-dev] Uploading Binary Files into Galaxy

2011-05-06 Thread Hans-Rudolf Hotz
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:

Re: [galaxy-dev] quick question: how can i supply the user's email address to a tool?

2011-05-06 Thread Peter Cock
On Fri, May 6, 2011 at 8:18 AM, Hans-Rudolf Hotz h...@fmi.ch 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

[galaxy-dev] options from file

2011-05-06 Thread SHAUN WEBB
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

Re: [galaxy-dev] options from file

2011-05-06 Thread Peter Cock
On Fri, May 6, 2011 at 10:17 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk 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

[galaxy-dev] typo in galaxy-dist/tool_conf.xml?

2011-05-06 Thread Marina Gourtovaia
Line 298 of galaxy-dist/tool_conf.xml in the zipped distribution downloaded yesterday tool file=indels/indel_table.xml / should be tool file=indels/indel_table.xml / ? Marina -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England

Re: [galaxy-dev] Restoring galaxy database return few empty tables.

2011-05-06 Thread Nate Coraor
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 on

Re: [galaxy-dev] Problem downloading file from local Galaxy

2011-05-06 Thread Nate Coraor
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 the

Re: [galaxy-dev] Workflow steps stuck in job queue - since cleanup_datasets.py

2011-05-06 Thread Nate Coraor
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 python

Re: [galaxy-dev] Question on setting metadata on upload via API

2011-05-06 Thread Nate Coraor
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 with

Re: [galaxy-dev] quick question: how can i supply the user's email address to a tool?

2011-05-06 Thread Nate Coraor
Peter Cock wrote: On Fri, May 6, 2011 at 8:18 AM, Hans-Rudolf Hotz h...@fmi.ch 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,

Re: [galaxy-dev] typo in galaxy-dist/tool_conf.xml?

2011-05-06 Thread Nate Coraor
Marina Gourtovaia wrote: Line 298 of galaxy-dist/tool_conf.xml in the zipped distribution downloaded yesterday tool file=indels/indel_table.xml / should be tool file=indels/indel_table.xml / ? Hi Marina, Indeed, thanks for catching this. It has been fixed and will go out in the

Re: [galaxy-dev] Problem downloading file from local Galaxy

2011-05-06 Thread Marco Moretto
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

Re: [galaxy-dev] Question on setting metadata on upload via API

2011-05-06 Thread Duddy, John
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

Re: [galaxy-dev] Question on setting metadata on upload via API

2011-05-06 Thread Nate Coraor
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 metadata on

Re: [galaxy-dev] Automatically sending an email to users you've shared a history with

2011-05-06 Thread Jennifer Jackson
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

[galaxy-dev] Unable to set metadata in API call

2011-05-06 Thread Duddy, John
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

Re: [galaxy-dev] quick question: how can i supply the user's email address to a tool?

2011-05-06 Thread Edward Kirton
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 n...@bx.psu.edu wrote: __tool_data_path__ = GALAXY_DATA_INDEX_DIR =

Re: [galaxy-dev] Bowtie why it does not take the 1_sequence.txt nor for bowtie nor the Convert

2011-05-06 Thread Jennifer Jackson
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

Re: [galaxy-dev] quick question: how can i supply the user's email address to a tool?

2011-05-06 Thread Nate Coraor
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 may