Hi Greg,

When I upload my workload ga file to galaxy, I get a screen saying that some of the tools in the workflow are not available in this instance of galaxy, specifically fastqc. I downloaded fastqc into my tools directory and restarted galaxy, but when I tried to re-upload the workflow it complained again that fastqc wasn't available. Fastqc does in fact load in the tools sidebar, but when I try to run it I get the following:

An error occurred running this job: Fastq failed.
Error executing FastQC. /bin/sh: fastqc: command not found

-Rob

On Mon, Apr 16, 2012 at 10:21 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:

Hi Rob,

When you import a workflow into a Galaxy instance, the instance must have all tools required by the workflow available in its tool panel.  I've only seen this error when the workflow requires a tool that is not available, so can you let us know if this is the case?

Thanks,

Greg Von Kuster

On Apr 16, 2012, at 10:07 AM, Robert Chase wrote:

Hi Greg,

After I modified the modules.py file that bug went away, but now I'm getting a new error:

Module galaxy.web.base.controller:420 in get_stored_workflow_steps         view
<<                  module = module_factory.from_workflow_step( trans, step )
                    #Check if tool was upgraded
                    step.upgrade_messages = module.check_and_update_state()
                    # Any connected input needs to have value DummyDataset (these
                    # are not persisted so we need to do it every time)>>  step.upgrade_messages = module.check_and_update_state()

AttributeError: 'NoneType' object has no attribute 'check_and_update_state'

-Rob

On Mon, Apr 16, 2012 at 9:19 AM, Robert Chase <rerpc@channing.harvard.edu> wrote:

Thanks Greg,

I'll try to merge the change into my version.

-Rob

On Mon, Apr 16, 2012 at 9:18 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:

Hello Robert,

Thanks for reporting this issue - it has been fixed in change set 7038:1fdcce63a06f, which is currently available only in our central repository.  It will be available in the dist in the next update.

Greg Von Kuster

On Apr 13, 2012, at 5:22 PM, Robert Chase wrote:

Hello All,

I'm pretty sure I found a bug in the main galaxy distribution. The following code diff shows the introduction of the line

tool_version = self.__get_tool_version( trans, tool_id )

but if you look at the function definition containing that line, you see

def from_workflow_step( Class, trans, step ):

which does not half a self in it. Then we get an error.

https://bitbucket.org/galaxy/galaxy-dist/diff/lib/galaxy/workflow/modules.py?diff2=e6464387ed3f&diff1=c60760713d26

-Rob

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