Hello,

When adding a new tool, we used a cheetah'ed shell script defined in the <configfiles> tags of the tool's xml file. To get the absolute path of an external script located in the tools directory, I used the following code in the <configfile> script:


${ os.getcwd() }/${ $__app__.config.tool_path }/toolsubdir/scriptname.sh

When I tried the new tool, I got an error message. Here are the last lines:

File "/g/funcgen/galaxy/lib/galaxy/tools/parameters/basic.py", line 681, in value_from_basic if isinstance( value, dict ) and value["__class__"] == "UnvalidatedValue":
KeyError: '__class__'

Therefore I slightly modified the file basic.py. I replaced the line 681:

if isinstance( value, dict ) and value["__class__"] == "UnvalidatedValue":

by:

if isinstance( value, dict ) and getattr(value, "__class__") == "UnvalidatedValue":

and it works fine now.
I fail to see why the original code didn't work though.
Hope that helps.

Regards,
L-A
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to