Forgot to 'reply-to-list', sorry:

Hi Peter

I think that package_perl_5_18 in the tool shed is broken, I came across the same error last week on both our production instance and a local 'test' instance (both v15.10).

My suspicion is that the following lines are to blame:

...
<action sha256sum="5c69adb47ab828aa3e8b5be89b88cd49c6a0d0dae2e8b3bca17a9ce699190e7b" type="download_file">
http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz
                </action>
<action type="shell_command">tar xfvz local-lib-1.008009.tar.gz</action>
...

Looking at the Galaxy internals I believe that the 'download_file' action automatically unpacks the archive and cd's into the resulting directory, hence the failure for the subsequent 'tar xfvz ...' command. But I haven't had the time yet to verify this or create a patch to see if the removal of this line addresses the problem.

I don't think I've seen the problem with 'package_gnu_coreutils_8_22' that you describe however so it may be that my hypothesis is not correct.

HTH

Best wishes

Peter

On 22/02/16 05:10, Peter van Heusden wrote:
Hi there Eric and others

I tried to install the JBrowse tool on a dev branch server running on an
Ubuntu 14.04 VM.

It got stuck at the package_gnu_coreutils_8_22 dependency (revision
ac64dfe4b1fb) - this ended up in "Installing tool dependencies" state.

If I go look at the tool details it highlights errors
in package_perl_5_18 which in turn refers to errors in gnu_coreutils
(just "Error" state) and then this more informative failure for perl:

"tar (child): local-lib-1.008009.tar.gz: Cannot open: No such file or
directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now"

I wonder if this is a sign of a download error?

Digging a bit more I find the error "Shutting down process id 21094
because it generated no output for the defined timeout period of 3600.0
seconds." for gnu_coreutils.

I'm trying to do a reinstall of the gnu_coreutils and perl packages to
see if I can get further.

Peter


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--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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