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> 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>> 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>> 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 >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> >> >> -- >> 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 >> >> >> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> >> > -- > 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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