Hello Eleanor,

it seems there are multiple issues present.

First of all in the 15.05 release the static/scripts/packed folder has been
changed to a symlink aiming at static/scripts (this is a part of internal
scriptbuild transition). If it is not a symlink in your filesystem you can
safely remove that folder (static/scripts/packed) with its contents and
update again to receive the correct symlink. That should help you with the
merging of the update.

Once updated (and please let us know if more trouble arise) we can start
troubleshooting why you canot connect to the Tool Shed (TS). Are you trying
to 'Search and browse tool sheds' in the Admin menu? What is your Galaxy
setup? Are you behind any proxy? What changed since the point at which you
were able to reach TS?

When it comes to the tophat2 error: the log that can tell you more is (by
default) printed in the console window in which you run Galaxy. If tophat
fails you should see some exceptions or at least a more explicit error
there.

As a side note it is good to know that the tophat you have locally
installed on your machine is probably not the tophat Galaxy is using while
running the tophat tool. Galaxy will try to use the TS tophat dependency
installed from the package_tophat2_2_0_9.

Please let us know how it goes.

Thank you

Martin, Galaxy Team


On Tue, May 19, 2015 at 11:28 PM Eleanor Morgan <e.mor...@curtin.edu.au>
wrote:

>   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.mor...@curtin.edu.au
> Web    | biomed.curtin.edu.au
>
>
>
>  Curtin University is a trademark of Curtin University of Technology.
> CRICOS Provider Code 00301J (WA), 02637B (NSW)
>
>
>   From: Eleanor Morgan <e.mor...@curtin.edu.au>
> Date: Tuesday, 19 May 2015 9:50 pm
> To: "galaxy-...@lists.bx.psu.edu" <galaxy-...@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.mor...@curtin.edu.au
> Web    | biomed.curtin.edu.au
>
>
>
>  Curtin University is a trademark of Curtin University of Technology.
> CRICOS Provider Code 00301J (WA), 02637B (NSW)
>
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