I am going to assume that you are working with a local instance, but
please correct us if that is wrong. Going forward, you will want to ask
local install questions at: galaxy-dev(a)bx.psu.edu, as that is where the
development community is most active.
Have you installed the FastQC binary already? This is required. The page
that Ross sent explains where to obtain binaries and the instructions at
each site define how to install the 3rd party tools. Here is the page again.
Help for making sure that paths are correctly set up is here. If you are
having an error, but the tool is installed, perhaps a path is incorrect.
Or if is correct, as a first pass: check for symbolic links and change
them to hard links. Then restart and see if that helps.
The general guidelines are that if you are having tool install problems,
make sure that the first is fully installed, then that the second is
organized correctly. If you need help with the second, use the
galaxy-dev(a)bx.psu.edu mailing list to ask specific questions, being sure
to include details about the paths/setup you have done so far.
When you are installing tools from the tool shed, these are the
Please be aware that certain tools may only run on larger servers (just
as they would if used on the line-command), and that configuration for
certain tools will require a production set-up, also as Ross noted. If
you are a biologist and want a simpler set up that is scalable, a cloud
Galaxy can be a great option:
But here are all:
Hopefully this helps get you going in the right direction,
On 12/9/13 5:38 AM, Jorge Braun wrote:
thanks for the information Ross but I'm lost with the guide for
fastqc tool. I don't understand how to resolve "missing tool dependecies"
Date: Mon, 9 Dec 2013 22:30:58 +1100
Subject: Re: [galaxy-user] Problem with executable file in FastQC
Galaxy source includes the Galaxy interfaces but not the third party
executables for tools like fastqc or bwa. They can be automagically
installed if you install the tool from a tool shed but at a guess, you
are working on your desktop with the fastqc tool in a recent clone of
galaxy? Unfortunately, the tool can't run until you have the fastqc
software working in a particular way hinted at in the guide for the
fastqc tool on the page at
There are things to do to make your instance more reliable and stable
too - eg
On Mon, Dec 9, 2013 at 9:48 PM, Jorge Braun <braun_bio(a)hotmail.com
I have a problem with Galaxy... FastQC doesn't run because the
file FastQC.py cann't find executable file FastQC.xml. Almost,
that file is in the same directory called rgenetics, (seeing Linux
someone can help me?
thanks and have a nice day :)
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