There are a couple groups working on improved trinity wrappers - I don't think they have reach the tool sheds though :(. As for the details of your specific tool - I think I would really need to see the tool to guess at the issue. Would it be possible to send us the problematic tool XML file or paste it to a service like gist.github.com? As for reloading the tool - if you add yourself as an admin user in galaxy's config/galaxy.ini file you should see a "Reload Tool Configuration" option in the admin menu that will allow you to manually reload the tool without restarting Galaxy (I generally recommend keeping this open in its own tab). Newer versions of Galaxy have some more experimental features designed to help as well - for instance if you create a virtualenv for Galaxy and install watchdog ("pip install watchdog") into it and then enable "watch_tools = True " in config/galaxy.ini Galaxy should automatically reload tools each time the tool config is updated. I am not sure anyone is really using this feature so it might still have some bugs (in particular I have noticed if the tool panel is really full there are problems so trimming that down might be required to use it). For the rare person like me who really hates using GUIs at all during development - you might also want to write some tests for the tool and run them using planemo (http://planemo.readthedocs.org/). It allows linting and testing tools without a Galaxy interface so you can be pretty confident the tool is working by the time you actually load it into a web browser and view it. -John On Mon, Jan 12, 2015 at 9:36 AM, Francis, Warren <w.francis@lrz.uni-muenchen.de> wrote:

Hello, I'm getting a strange error when trying to debug a tool.

Traceback (most recent call last): File "/var/project/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 157, in prepare_job job_wrapper.prepare() File "/var/project/galaxy-dist/lib/galaxy/jobs/__init__.py", line 811, in prepare self.command_line, self.extra_filenames = tool_evaluator.build() File "/var/project/galaxy-dist/lib/galaxy/tools/evaluation.py", line 348, in build self.__build_command_line( ) File "/var/project/galaxy-dist/lib/galaxy/tools/evaluation.py", line 364, in __build_command_line command_line = fill_template( command, context=param_dict ) File "/var/project/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/var/project/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1421072368_91_78155.py", line 139, in respond EOFError: EOF when reading a line

The tool is the assembler Trinity. The toolshed version is quite old and the one from the Trinity website does not work, so I tried to fix it (several problems to fix).

What is the EOFError? There were a bunch of posts reporting this but no answer as to why this happens.

Is there a way to debug a tool without having to restart galaxy each time? Something offline that can check for runtime errors, or at least see if it generates the command correctly.

Best, -Warren ___________________________________________________________ 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: https://lists.galaxyproject.org/

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