I'm guessing FastQC isn't installed by default? This page give these instructions: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies FastQC (0.10.0)NGS: QC and manipulationFastQC from Babraham. The main fastqc perl script must be executable from tool-data/shared/jars/FastQC/fastqc But I don't understand what it means. Do I need to download something, change permissions? I don't have anything inside the jars folder. Thanks, Greg
Hi Greg, Indeed you need to install many many tools to make galaxy run. You may be better off getting the cloud version, which has many tools already installed. Getting GALAXY to run with all the tools that are provided is not a trivial task... It gets MUCH better with the TOOLSHED option, since this can install many of the tools you may need... the "old" way of galaxy was to rely on many of the tools to be available on the path so they magically run, but things like GATK and FASTQC etc. that are run from JAVA jars, need to be installed manually into that directory tool-data/shared/jars Thon On Dec 06, 2012, at 11:36 AM, greg <margeemail@gmail.com> wrote: I'm guessing FastQC isn't installed by default? This page give these instructions: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies FastQC (0.10.0)NGS: QC and manipulationFastQC from Babraham. The main fastqc perl script must be executable from tool-data/shared/jars/FastQC/fastqc But I don't understand what it means. Do I need to download something, change permissions? I don't have anything inside the jars folder. Thanks, Greg ___________________________________________________________ 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/
Thanks Thon. What is the TOOLSHED option? As far as FASTQC, I downloaded and extracted it, but now what? Do I dump all of those files and directories in tool-data/shared/jars?
wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip unzip fastqc_v0.10.1.zip ls FastQC/ Contaminants fastqc fastqc_icon.ico Help INSTALL.txt jbzip2-0.9.jar LICENSE.txt README.txt RELEASE_NOTES.txt run_fastqc.bat sam-1.32.jar Templates uk
Thanks, Greg On Thu, Dec 6, 2012 at 6:40 PM, Anthonius deBoer <thondeboer@me.com> wrote:
Hi Greg,
Indeed you need to install many many tools to make galaxy run. You may be better off getting the cloud version, which has many tools already installed. Getting GALAXY to run with all the tools that are provided is not a trivial task...
It gets MUCH better with the TOOLSHED option, since this can install many of the tools you may need... the "old" way of galaxy was to rely on many of the tools to be available on the path so they magically run, but things like GATK and FASTQC etc. that are run from JAVA jars, need to be installed manually into that directory tool-data/shared/jars
Thon
On Dec 06, 2012, at 11:36 AM, greg <margeemail@gmail.com> wrote:
I'm guessing FastQC isn't installed by default?
This page give these instructions: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
FastQC (0.10.0)NGS: QC and manipulationFastQC from Babraham. The main fastqc perl script must be executable from tool-data/shared/jars/FastQC/fastqc
But I don't understand what it means. Do I need to download something, change permissions? I don't have anything inside the jars folder.
Thanks,
Greg ___________________________________________________________ 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:
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