HI Jorge,
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-...@bx.psu.edu, as that is where the
development community is most active.
Lists: http://wiki.galaxyproject.org/MailingLists
Search: http://galaxyproject.org/search/getgalaxy/
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.
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
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.
http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
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-...@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
instructions:
http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy
http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
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:
http://usegalaxy.org/cloud
But here are all:
http://wiki.galaxyproject.org/BigPicture/Choices
Hopefully this helps get you going in the right direction,
Jen
Galaxy team
On 12/9/13 5:38 AM, Jorge Braun wrote:
thanks for the information Ross but I'm lost with the guide for the
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
From: ross.laza...@gmail.com
To: braun_...@hotmail.com
CC: galaxy-user@lists.bx.psu.edu
Hi, Jorge,
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
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies - try
that please?
There are things to do to make your instance more reliable and stable
too - eg
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
On Mon, Dec 9, 2013 at 9:48 PM, Jorge Braun braun_...@hotmail.com
mailto:braun_...@hotmail.com wrote:
Hi mates!!
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
terminal) .
someone can help me?
thanks and have a nice day :)
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
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