Hi Dannon,

I tried to run Bowtie2 and Tophat using a reference from history and these
are the errors I got:

*An error occurred running this job: Error indexing reference sequence
/bin/sh: bowtie2-build: command not found.*
*
*
*
*
*An error occurred running this job: Could not determine Tophat version
/bin/sh: tophat: command not found Error indexing reference sequence
/bin/sh: bowtie-build: command not found cp:
/Users/abebe/tabix-0.2.6/python/galaxy-dist/database/job_working_directory/000/65/tophat_out/insertions.b
*
*
*
I also tried to run eXpress on data mapped using Bowtie and this error came:

*An error occurred running this job: /bin/sh: express: command not found
cp:
/Users/abebe/tabix-0.2.6/python/galaxy-dist/database/job_working_directory/000/63/params.xprs:
No such file or directory cp:
/Users/abebe/tabix-0.2.6/python/galaxy-dist/database/job_working_directory/000/63/results.
*

External dependencies might be the problem. We didn't do anything to
install NGS tools or others for that matter. How do we install dependencies?


Thanks for your help.

Tilahun
--------------------------

On Tue, Dec 18, 2012 at 10:32 AM, Dannon Baker <dannonba...@me.com> wrote:

> What specific errors are you seeing?  Some tools have external
> dependencies that need to be installed.
>
> -Dannon
>
> On Dec 18, 2012, at 11:29 AM, Tilahun Abebe <tilahun.ab...@uni.edu> wrote:
>
> > Hi,
> >
> > We installed a local galaxy a couple of days ago following the basic
> installation instruction (http://wiki.galaxyproject.org/Admin/Get%20Galaxy).
> The installation went well, all the tools are listed on the left. I can
> also upload data to Galaxy. However, an error occurs when I try to run
> RNA-seq analysis. I am thinking the tools are not configured properly. Can
> you give me tips to configure NGS tools? An example file with setup syntax
> will help as well.
> >
> > Thanks.
> >
> > Tilahun
> > ___________________________________________________________
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