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: 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: 2.1.0.0 [2015-05-19 21:15:11] Checking for Samtools S 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 Eleanor Morgan Senior Scientific Officer | School of Biomedical Sciences | Faculty of Health Sciences Curtin University Tel | +61 8 9266 7516 Mob | +61 408 004 369 Fax | +61 8 9266 2342 Email | e.morgan@curtin.edu.au<mailto:e.morgan@curtin.edu.au> Web | biomed.curtin.edu.au [cid:73AB5085-67E7-491A-AC7A-694821970AA3] Curtin University is a trademark of Curtin University of Technology. CRICOS Provider Code 00301J (WA), 02637B (NSW)