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
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
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
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
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.
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:
Interactivehttp://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#
(full)
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,
