Robert,

It sounds like you're experiencing two separate problems to me.  Let's 
isolating the problem to just the FastQC tool install, first, and move on from 
there.  There is a FastQC tool in your toolbar, and execution results in the 
error you describe in the previous email of 'Fastq failed.  Error executing 
FastQC. /bin/sh: fastqc command not found'.  Correct?

If this is the case, can you verify that you do have fastqc installed and 
accessible on the path of the galaxy user?  And, how did you add the tool to 
galaxy- via toolshed or did you use the FastQC wrapper included with the 
primary Galaxy distribution?

-Dannon


On Apr 16, 2012, at 6:23 PM, Greg Von Kuster wrote:

> Hi Robert,
> 
> I've cc'd the galaxy-dev list on this reply since the workflow components are 
> primarily supported by other Galaxy development team members and I'm not 
> optimally suited to handle this issue.  Please keep responses on the 
> galaxy-dev mail list so others that are interested can follow the entire 
> thread.  You should receive a response on this soon.
> 
> Thanks for sending your messages,
> 
> Greg Von Kuster
> 
> On Apr 16, 2012, at 5:53 PM, Robert Chase wrote:
> 
>> 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 <g...@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 <re...@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 <g...@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
>>>> ___________________________________________________________
>>>> Please keep all replies on the list by using "reply all"
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>>>> 
>>>>  http://lists.bx.psu.edu/
>>> 
>>> 
>>> 
>> 
>> 
> 
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