Hi again,
I didn’t get any response to this so decided to try an upgrade in the hope that I could reestablish access to the toolshed. I used bitbucket because I was unsure of the implications if I moved to github. Here are the commands I issued:
su – galaxy
cd /galaxy/galaxy-dist/
hg pull
hg update latest_15.05
I was repeatedly asked questions re changing or deleting various scripts:
local changed static/scripts/packed/mvc/data.js which remote deleted
use (c)hanged version or (d)elete? C
I chose c for all of these
Once that finished, the merging process began but eventually ended in an error message:
merging static/scripts/nls/zh/locale.js
abort: could not symlink to './': File exists: /galaxy/galaxy-dist/static/scripts/packed
Any help with this error would be greatly appreciated. Last time I updated, I did this from within the galaxy-dist directory (/galaxy/galaxy-dist) rather than the root /galaxy directory and it worked. Is that correct?
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.aumailto:e.morgan@curtin.edu.au Web | biomed.curtin.edu.au
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From: Eleanor Morgan <e.morgan@curtin.edu.aumailto:e.morgan@curtin.edu.au> Date: Tuesday, 19 May 2015 9:50 pm To: "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] tophat2 failing to execute
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.aumailto:e.morgan@curtin.edu.au Web | biomed.curtin.edu.au
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