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_bio@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 :)

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-dev@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-dev@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_unin...

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"

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Date: Mon, 9 Dec 2013 22:30:58 +1100 Subject: Re: [galaxy-user] Problem with executable file in FastQC From: ross.lazarus@gmail.com To: braun_bio@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_bio@hotmail.com mailto:braun_bio@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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