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.mor...@curtin.edu.au<mailto:e.mor...@curtin.edu.au>
Web | biomed.curtin.edu.au
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