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 <dannonba...@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.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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