Thanks Peter - this specific package has now been fixed in the toolsheds and 
should work without patching the Galaxy code.

I understand that more generally Nicola is working on applying the same fix 
(removing whitespace around the target URL when using the "download_file" 
action) in other packages that might be similarly affected.

Big thanks to Bjoern, Marius and Nicola for their efforts in sorting this out.

Peter

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

________________________________
From: Peter van Heusden [p...@sanbi.ac.za]
Sent: Thursday, February 25, 2016 4:17 PM
To: Peter Briggs
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: Broken package_perl_5_18, was Re: [galaxy-dev] JBrowse on dev 
branch: progress


I knew there was an email that I forgot to send! Nicola Soranzo fixed this with 
galaxy PR https://github.com/galaxyproject/galaxy/pull/1775 - sometime in 
November last year Eric added whitespace to the perl package (and a bunch of 
other things) that broke the download_file action, so Nicola's patch strips 
whitespace. (The conversation about this happened on IRC and the PR)

I tested the PR and it makes the perl install work (which makes the JBrowse 
installl work, yay!).

Peter

On 25 Feb 2016 6:10 PM, "Peter Briggs" 
<peter.bri...@manchester.ac.uk<mailto:peter.bri...@manchester.ac.uk>> wrote:
Hello Peter

Re the failing install of 'package_perl_5_18', I've investigated further now 
and have submitted a patch which seems to fix the problem:

https://github.com/galaxyproject/tools-iuc/pull/616

Not sure if this is of any immediate help,

Best wishes

Peter

On 22/02/16 09:43, Peter van Heusden wrote:
Ok, second attempt, perl install died with the same error, so I suspect
you're right about the cause. Eric?

Peter

On 22 February 2016 at 11:41, Peter van Heusden 
<p...@sanbi.ac.za<mailto:p...@sanbi.ac.za>
<mailto:p...@sanbi.ac.za<mailto:p...@sanbi.ac.za>>> wrote:

    Thanks Peter

    I managed, on the second attempt, to get past the gnu coreutils
    problem. Zipho noticed a weird lockup though: conftest that seemed
    to be from the gnu coreutils install wanted to listen on port 4001,
    which is the same port our uwsgi server listens on. The install has
    now completed but I'll try and find time to go back and verify this.

    On the second attempt perl seems to be installing, so I'll see if it
    completes or hits the error you're mentioning.

    Peter

    On 22 February 2016 at 11:34, Peter Briggs
    <peter.bri...@manchester.ac.uk<mailto:peter.bri...@manchester.ac.uk>
    
<mailto:peter.bri...@manchester.ac.uk<mailto:peter.bri...@manchester.ac.uk>>> 
wrote:

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





___________________________________________________________
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--
Peter Briggs peter.bri...@manchester.ac.uk<mailto:peter.bri...@manchester.ac.uk>
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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  https://lists.galaxyproject.org/

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