is there a variable i can use in the tool config xml file? thanks! ed
Hi Ed
You can use the variable "$userEmail" in the 'command' tag of the tool definition file
Regards, Hans
On 05/06/2011 03:56 AM, Edward Kirton wrote:
is there a variable i can use in the tool config xml file? thanks! ed
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On Fri, May 6, 2011 at 8:18 AM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Ed
You can use the variable "$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 there any other similar variables worth knowing about?
Peter
Peter Cock wrote:
On Fri, May 6, 2011 at 8:18 AM, Hans-Rudolf Hotz hrh@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 there any other similar variables worth knowing about?
Yes. I added these to the wiki under the <command> section. Also, since they used 3 different naming styles, I changed them all to use the pythonic standard for constants and reserved names, but the old names are maintained for backwards-compatibility.
__new_file_path__ = universe_wsgi.ini new_file_path value __tool_data_path__ = GALAXY_DATA_INDEX_DIR = universe_wsgi.ini tool_data_path value __root_dir__ = GALAXY_ROOT_DIR = Top-level Galaxy source directory made absolute via os.path.abspath() __datatypes_config__ = GALAXY_DATATYPES_CONF_FILE = universe_wsgi.ini datatypes_config value __user_id__ = userId = Email's numeric ID (id column of galaxy_user table in the database) __user_email__ = userEmail = User's email address __app__ = The galaxy.app.UniverseApplication instance, gives access to __app__.config and much more. Should be used as a last resort, may go away in future releases.
The new names will be available in the next stable release, which is looking like it will be out next week.
--nate
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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 nate@bx.psu.edu wrote:
__tool_data_path__ = GALAXY_DATA_INDEX_DIR = universe_wsgi.ini tool_data_path value
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 not, when in doubt, look in lib/galaxy/config.py.
--nate
Thanks!
On Fri, May 6, 2011 at 9:06 AM, Nate Coraor nate@bx.psu.edu wrote:
__tool_data_path__ = GALAXY_DATA_INDEX_DIR = universe_wsgi.ini tool_data_path value
awesome; thanks everyone for your help.
On Fri, May 6, 2011 at 9:03 PM, Nate Coraor nate@bx.psu.edu wrote:
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 not, when in doubt, look in lib/galaxy/config.py.
--nate
Thanks!
On Fri, May 6, 2011 at 9:06 AM, Nate Coraor nate@bx.psu.edu wrote:
__tool_data_path__ = GALAXY_DATA_INDEX_DIR = universe_wsgi.ini tool_data_path value
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Nate Coraor -
Peter Cock