Colin;
Second -and still unsolved- problem: When i try to run a picard tool, I get the following exception:
File "/home/hg/Galaxy/galaxy-dist/tools/picard/picard_wrapper.py", line 40 class PicardBase(): ^ SyntaxError: invalid syntax
What version of Python are you running? This appears to be a syntax error from an older version: $ python2.7 Python 2.7.1+ (r271:86832, Apr 11 2011, 18:13:53) [GCC 4.5.2] on linux2 Type "help", "copyright", "credits" or "license" for more information.
class Test(): ...
$ python2.4 Python 2.4.3 (#1, Nov 11 2010, 13:30:19) [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
class Test(): File "<stdin>", line 1 class Test(): ^ SyntaxError: invalid syntax
If you're using 2.4 it's well worth upgrading to 2.6 or 2.7. Hope this helps, Brad