Question: TopHat Error stating that (installed) Bowtie2 is not installed
gravatar for mohammedtleis
4 months ago by
mohammedtleis0 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. 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/ 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

ADD COMMENTlink written 4 months ago by mohammedtleis0
gravatar for Devon Ryan
4 months ago by
Devon Ryan1.6k
Devon Ryan1.6k wrote:
  1. Have a look for an file in a tophat directory under tool_deps/, sometimes those go missing.
  2. Switch to conda for dependency resolution, it makes life SO much easier.
  3. Don't use tophat for any new analyses. STAR is the probably the best aligner to use and it works well in Galaxy. If the memory requirements are too high, then use hisat2 instead. Regardless, don't use tophat.
ADD COMMENTlink written 4 months ago by Devon Ryan1.6k

Cross-reference with

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson22k
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