Tools appearing without inputs in workflow editor
A colleague of mine posted this on the Users list ... 4 days later and no replies! I'm hoping that one of the Devs can shed a bit of light ------------------------------------------------------------------------ --------------------------------------------------- A peculiar bug, presented for your input: A colleague has built a few tools and is trying to incorporate them into a workflow. However: 1. When he creates an new empty workflow, edits it and adds the tools, they appear without inputs (i.e. the icons/boxes on the diagram have no input "sockets") 2. When he tries to save a history using these tools as a workflow, a error results in which Galaxy complains about an unrecognised name, being one of the tool inputs. Depending on which tool he includes in the workflow, the missing name occurs in whichever tool is earlier in the workflow. (Traceback available on request) Puzzling. And even more puzzling when I tried to debug this: 1. Other tools (not written by him) behave in the workflows as expected. 2. Pulling a copy of his config file across to my own instance of Galaxy and creating a dummy tool to house it, it worked perfectly 3. We're running the same version of Galaxy, albeit different versions of Python (2.5 vs 2.6.4) 4. The tools work fine in normal analysis mode. 5. Line-ending unix, XML seems to parse fine. I'm stymied here and unsure what to look at next. Ideas? ------------------------------------------------------------------------ --------------------------------------------------- Thanks Steve Dr Steven Platt Bioinformatician Health Protection Agency Microbiology Services Division London www.hpa.org.uk/bioinformatics ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************
Could you send me the traceback and perhaps a copy of the misbehaving tool config files? I'll be happy to take a look. Thanks! Dannon On Nov 21, 2011, at 9:53 AM, Steven Platt wrote:
A colleague of mine posted this on the Users list ... 4 days later and no replies! I'm hoping that one of the Devs can shed a bit of light ------------------------------------------------------------------------ --------------------------------------------------- A peculiar bug, presented for your input:
A colleague has built a few tools and is trying to incorporate them into a workflow. However:
1. When he creates an new empty workflow, edits it and adds the tools, they appear without inputs (i.e. the icons/boxes on the diagram have no input "sockets") 2. When he tries to save a history using these tools as a workflow, a error results in which Galaxy complains about an unrecognised name, being one of the tool inputs. Depending on which tool he includes in the workflow, the missing name occurs in whichever tool is earlier in the workflow. (Traceback available on request)
Puzzling. And even more puzzling when I tried to debug this: 1. Other tools (not written by him) behave in the workflows as expected. 2. Pulling a copy of his config file across to my own instance of Galaxy and creating a dummy tool to house it, it worked perfectly 3. We're running the same version of Galaxy, albeit different versions of Python (2.5 vs 2.6.4) 4. The tools work fine in normal analysis mode. 5. Line-ending unix, XML seems to parse fine.
I'm stymied here and unsure what to look at next. Ideas? ------------------------------------------------------------------------ ---------------------------------------------------
Thanks
Steve
Dr Steven Platt Bioinformatician Health Protection Agency Microbiology Services Division London www.hpa.org.uk/bioinformatics ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************
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Dannon, Thanks for agreeing to have a look at this. Configs and traceback are attached. Just to clarify, these tools work without error when run individually, and it's only when we try and generate a workflow that problems occur. Cheers Steve -----Original Message----- From: Dannon Baker [mailto:dannonbaker@me.com] Sent: 21 November 2011 15:28 To: Steven Platt Cc: galaxy-dev@lists.bx.psu.edu; Paul-Michael Agapow Subject: Re: [galaxy-dev] Tools appearing without inputs in workflow editor Could you send me the traceback and perhaps a copy of the misbehaving tool config files? I'll be happy to take a look. Thanks! Dannon On Nov 21, 2011, at 9:53 AM, Steven Platt wrote:
A colleague of mine posted this on the Users list ... 4 days later and no replies! I'm hoping that one of the Devs can shed a bit of light
------------------------------------------------------------------------
--------------------------------------------------- A peculiar bug, presented for your input:
A colleague has built a few tools and is trying to incorporate them into a workflow. However:
1. When he creates an new empty workflow, edits it and adds the tools, they appear without inputs (i.e. the icons/boxes on the diagram have no input "sockets") 2. When he tries to save a history using these tools as a workflow, a error results in which Galaxy complains about an unrecognised name, being one of the tool inputs. Depending on which tool he includes in the workflow, the missing name occurs in whichever tool is earlier in the workflow. (Traceback available on request)
Puzzling. And even more puzzling when I tried to debug this: 1. Other tools (not written by him) behave in the workflows as expected. 2. Pulling a copy of his config file across to my own instance of Galaxy and creating a dummy tool to house it, it worked perfectly 3. We're running the same version of Galaxy, albeit different versions of Python (2.5 vs 2.6.4) 4. The tools work fine in normal analysis mode. 5. Line-ending unix, XML seems to parse fine.
I'm stymied here and unsure what to look at next. Ideas?
------------------------------------------------------------------------
---------------------------------------------------
Thanks
Steve
Dr Steven Platt Bioinformatician Health Protection Agency Microbiology Services Division London www.hpa.org.uk/bioinformatics -----------------------------------------
************************************************************************ **
The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk
************************************************************************ **
___________________________________________________________ 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:
----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************
participants (2)
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Dannon Baker -
Steven Platt