Yep, that's the primary issue with tophat not being found -- you'll need to 
install binaries for some tools and potentially some reference genomes.

See the wiki page here for lots more information: 
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup


On Dec 18, 2012, at 11:48 AM, Tilahun Abebe <tilahun.ab...@uni.edu> wrote:

> 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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> 

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