Hi Tilahun,
   What you can do is to download the tools and make symlinks to /usr/bin. You can download bowtie (http://bowtie-bio.sourceforge.net/manual.shtml), tophat (http://tophat.cbcb.umd.edu/) and cufflinks (http://cufflinks.cbcb.umd.edu/). Then after decompressing it, enter your terminal and enter make the symlinks. For example, for one of the bowtie files

sudo ln -s /home/path-to-the-directory-where-you-put-all-files/bowtie/bowtie /usr/bin/bowtie


   You have to create links to all executable files. You can make it in a text editor and simply copy in the terminal. Not sure if that the easiest way, but it works. If you get some permissions errors, you can change the permissions of the files you are making symlinks to.
Best,


Luciano


On Tue, Dec 18, 2012 at 10:55 AM, Dannon Baker <dannonbaker@me.com> wrote:
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.Abebe@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 <dannonbaker@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.abebe@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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