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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: