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 <dannonba...@me.com> 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 <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"
> >>>> 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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