Hello,

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 is:

I checked the tool_dependency.xml file

<tool_dependency>

  <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>

    <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>

    <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" />

    </package>

</tool_dependency>

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.

Regards,

Eleanor