Question: TopHat Error stating that (installed) Bowtie2 is not installed
0
mohammedtleis • 0 wrote:
I tried to try 'TopHat (v.2.1.0)' locally to align some RNA-Seq data to a reference human genome. The tools execution has failed stating that bowtie 2 is not found. However, Bowtie2 (v.2.3.0.1) is installed and I can verify it in my local tool shed (revision 937aa69e715f).
Here is the error after executing TopHat:
Fatal error: Tool execution failed
/Users/tleis/GitHub/galaxy/galaxy/database/jobs_directory/000/51/tool_script.sh: line 9: bowtie2-build: command not found
[2017-05-15 17:29:03] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2017-05-15 17:29:03] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.
Your help is highly appreciated
