Question: TopHat Error stating that (installed) Bowtie2 is not installed
0
gravatar for mohammedtleis
9 weeks 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.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

ADD COMMENTlink written 9 weeks ago by mohammedtleis0
1
gravatar for Devon Ryan
9 weeks ago by
Devon Ryan1.6k
Germany
Devon Ryan1.6k wrote:
  1. Have a look for an env.sh 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 9 weeks ago by Devon Ryan1.6k
1

Cross-reference with https://biostar.usegalaxy.org/p/23084/

ADD REPLYlink written 9 weeks ago by Jennifer Hillman Jackson22k
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