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:
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:
> 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:
> No such file or directory cp:
> 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.
> 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.
> 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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