Workflow import error

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Workflow import error

Robert Chase
Hello All,

I have just tried to import a workflow file and when I try to view the workflow, I'm getting an error, "global name 'self' is not defined".

Error Traceback:

View as:   Interactive (full)  |  Text (full)  |  XML (full)
NameError: global name 'self' is not defined
URL: http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e
Module weberror.evalexception.middleware:364 in respond         view
<<          try:
                __traceback_supplement__ = errormiddleware.Supplement, self, environ
                app_iter = self.application(environ, detect_start_response)
                try:
                    return_iter = list(app_iter)
>>  app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__         view
<<          try:
                status, headers, body = wsgilib.intercept_output(
                    environ, self.app)
                if status is None:
                    # Some error occurred
>>  environ, self.app)
Module paste.wsgilib:539 in intercept_output         view
<<          data.append(headers)
            return output.write
        app_iter = application(environ, replacement_start_response)
        if data[0] is None:
            return (None, None, app_iter)
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__         view
<<          environ['paste.recursive.script_name'] = my_script_name
            try:
                return self.application(environ, start_response)
            except ForwardRequestException, e:
                middleware = CheckForRecursionMiddleware(
>>  return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__         view
<<                             []).append(HTTPException)
            try:
                return self.application(environ, start_response)
            except HTTPException, exc:
                return exc(environ, start_response)
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__         view
<<          kwargs.pop( '_', None )
            try:
                body = method( trans, **kwargs )
            except Exception, e:
                body = self.handle_controller_exception( e, trans, **kwargs )
>>  body = method( trans, **kwargs )
Module galaxy.web.controllers.workflow:207 in display_by_id         view
<<          # Get workflow.
            stored_workflow = self.get_stored_workflow( trans, id )
            return self.display(trans, stored_workflow)
   
        def display(self, trans, stored_workflow):
>>  return self.display(trans, stored_workflow)
Module galaxy.web.controllers.workflow:217 in display         view
<< 
            # Get data for workflow's steps.
            self.get_stored_workflow_steps( trans, stored_workflow )
            # Get annotations.
            stored_workflow.annotation = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, stored_workflow )
>>  self.get_stored_workflow_steps( trans, stored_workflow )
Module galaxy.web.base.controller:418 in get_stored_workflow_steps         view
<<              if step.type == 'tool' or step.type is None:
                    # Restore the tool state for the step
                    module = module_factory.from_workflow_step( trans, step )
                    #Check if tool was upgraded
                    step.upgrade_messages = module.check_and_update_state()
>>  module = module_factory.from_workflow_step( trans, step )
Module galaxy.workflow.modules:369 in from_workflow_step         view
<<          """
            type = step.type
            return self.module_types[type].from_workflow_step( trans, step )
       
    module_factory = WorkflowModuleFactory( dict( data_input=InputDataModule, tool=ToolModule ) )
>>  return self.module_types[type].from_workflow_step( trans, step )
Module galaxy.workflow.modules:202 in from_workflow_step         view
<<              # in addition to tool id, enhance the selection process here
                # to retrieve the correct version of the tool.
                tool_version = self.__get_tool_version( trans, tool_id )
                if tool_version:
                    tool_version_ids = tool_version.get_version_ids( trans.app )
>>  tool_version = self.__get_tool_version( trans, tool_id )
NameError: global name 'self' is not defined

Thankyou in advance for any help that you can give.

-Rob

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Re: Workflow import error

Robert Chase
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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Re: Workflow import error

Greg Von Kuster
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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and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/


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Re: Workflow import error

Greg Von Kuster
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 <[hidden email]> 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 <[hidden email]> 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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Re: Workflow import error

Greg Von Kuster
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 <[hidden email]> 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     <img src="x-msg://17/" border="0" height="9" width="9">     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 <[hidden email]> 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 <[hidden email]> 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"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/







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Re: Workflow import error

Dannon Baker
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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"
>>>> in your mail client.  To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>>
>>>>  http://lists.bx.psu.edu/
>>>
>>>
>>>
>>
>>
>
> ___________________________________________________________
> 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/

___________________________________________________________
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Re: Workflow import error

Robert Chase
Hello Dannon,

I have downloaded the fastqc compiled program from

http://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc

I have added the directory containing the program fastqc to the path. The source version gave an error.

Now I can successfully run the fastqc tool from the tool menu. I got this tool (the xml and python file) from the repository

http://toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc

I tried deleting the uploaded workflow and uploading it again. I still get a screen complaining that it requires tools that are not available. When I click on the button for the tools, it says that fastqc is not available.

The operative part of the .ga file is here I think:

            "tool_id": "fastqc",
            "tool_state": "{\"__page__\": 0, \"contaminants\": \"null\", \"chrom
Info\": \"\\\"/galaxy/home/g2main/galaxy_main/tool-data/shared/ucsc/chrom/hg19.l
en\\\"\", \"out_prefix\": \"\\\"FastQC\\\"\", \"input_file\": \"null\"}",
            "tool_version": "0.4",

When I look at the fastqc tool xml file I see that the version is 1.0.0

<tool id="FastQC" name="FastQC" version="1.0.0">
  <description>quality control checks on raw sequence data</description>
  <command interpreter="python">fastqc.py

Could it be a version problem? Does the capitalization of the tool id matter?

-Rob

On Mon, Apr 16, 2012 at 9:31 PM, Dannon Baker <[hidden email]> wrote:
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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"
>>>> in your mail client.  To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>>
>>>>  http://lists.bx.psu.edu/
>>>
>>>
>>>
>>
>>
>
> ___________________________________________________________
> 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/



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Re: Workflow import error

Ross-2
Hi, Robert.
This is a longstanding wart  - FastQC has to be invoked by a perl
script distributed by the Babraham people - called simply 'fastqc'.
To get this to work, the Galaxy FastQC wrapper expects that the FastQC
distribution archive has been unpacked to
tool-data/shared/jars/FastQC
under your local Galaxy root.

That means the fastqc perl script will be found at
tool-data/shared/jars/FastQC/fastqc
You will also need to make sure that the fastqc perl script that comes
in the FastQC distribution is executable - I think the archive is made
using windows so it needs tweaking to work under linux. Sorry this is
so specific but we haven't come up with a better way of dealing with
FastQC's specific requirements.

I hope this helps?

On Tue, Apr 17, 2012 at 4:12 PM, Robert Chase
<[hidden email]> wrote:

> Hello Dannon,
>
> I have downloaded the fastqc compiled program from
>
> http://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc
>
> I have added the directory containing the program fastqc to the path. The
> source version gave an error.
>
> Now I can successfully run the fastqc tool from the tool menu. I got this
> tool (the xml and python file) from the repository
>
> http://toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc
>
> I tried deleting the uploaded workflow and uploading it again. I still get a
> screen complaining that it requires tools that are not available. When I
> click on the button for the tools, it says that fastqc is not available.
>
> The operative part of the .ga file is here I think:
>
>             "tool_id": "fastqc",
>             "tool_state": "{\"__page__\": 0, \"contaminants\": \"null\",
> \"chrom
> Info\":
> \"\\\"/galaxy/home/g2main/galaxy_main/tool-data/shared/ucsc/chrom/hg19.l
> en\\\"\", \"out_prefix\": \"\\\"FastQC\\\"\", \"input_file\": \"null\"}",
>             "tool_version": "0.4",
>
> When I look at the fastqc tool xml file I see that the version is 1.0.0
>
> <tool id="FastQC" name="FastQC" version="1.0.0">
>   <description>quality control checks on raw sequence data</description>
>   <command interpreter="python">fastqc.py
>
> Could it be a version problem? Does the capitalization of the tool id
> matter?
>
> -Rob
>
>
> On Mon, Apr 16, 2012 at 9:31 PM, Dannon Baker <[hidden email]> wrote:
>>
>> 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 <[hidden email]>
>> >> 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
>> >>> <[hidden email]> 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 <[hidden email]>
>> >>> 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"
>> >>>> in your mail client.  To manage your subscriptions to this
>> >>>> and other Galaxy lists, please use the interface at:
>> >>>>
>> >>>>  http://lists.bx.psu.edu/
>> >>>
>> >>>
>> >>>
>> >>
>> >>
>> >
>> > ___________________________________________________________
>> > 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/
>>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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>  http://lists.bx.psu.edu/



--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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