I am running a local Galaxy install, last update was June, 2014 release.  I 
installed Tophat2 from the tool repository some months ago and the tool 
dependency packages for Bowtie2 and Samtools were also installed.  I have built 
bowtie2 indices on the human hg19 genome and can select this as the reference 
genome.  I am working through a tutorial with paired-end sequence reads that 
works fine on the main galaxy public server.  When I try to run it on my local 
instance, however, Tophat2 fails.  The error reported in the galaxy data window 
Fatal error: Tool execution failed

[2015-05-19 21:15:11] Beginning TopHat run (v2.0.9)
[2015-05-19 21:15:11] Checking for Bowtie
 Bowtie version:
[2015-05-19 21:15:11] Checking for Samtools

I checked the tool_dependency.xml file


  <package name="bowtie2" version="2.1.0">

      <repository changeset_revision="017a00c265f1" 
name="package_bowtie2_2_1_0" owner="devteam" 
prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu"; />


    <package name="samtools" version="0.1.18">

      <repository changeset_revision="171cd8bc208d" 
name="package_samtools_0_1_18" owner="devteam" 
prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu"; />


    <package name="tophat2" version="2.0.9">

      <repository changeset_revision="8549fd545473" 
name="package_tophat2_2_0_9" owner="devteam" 
prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu"; />



All of the listed packages appear to be installed.  I am unsure why in the run 
log it is checking for Bowtie instead of Bowtie2, although the version is 
correct for the Bowtie2 package that is installed.

I would like to reinstall everything, but can't get onto the toolshed anymore, 
I just get a message that I will be redirected, but nothing happens.

I am a newbie user of galaxy.  Can anyone direct me to a log file that might 
contain more information about why Tophat2 is failing to execute?  It works 
fine on the command line.

Thanks very much for any advice on what I should check next.



Eleanor Morgan
Senior Scientific Officer | School of Biomedical Sciences | Faculty of Health 

Curtin University
Tel    | +61 8 9266 7516
Mob  | +61 408 004 369
Fax    | +61 8 9266 2342
Email  | e.mor...@curtin.edu.au<mailto:e.mor...@curtin.edu.au>
Web    | biomed.curtin.edu.au


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