I now noticed that another repository I own also only works after I choose “reset all metadata” at Tool Shed. See
https://toolshed.g2.bx.psu.edu/view/pieterlukasse/primo_multiomics
This repository does not seem to have any problems... Could there be something wrong with Tool Shed and our version of Galaxy (incompatibility issues)? And
why would “reset all metadata” on tool shed solve the issue? Now for every commit I make, I seem to have to do this...strange.
Thanks,
Pieter
From: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org]
On Behalf Of Lukasse, Pieter
Sent: donderdag 19 maart 2015 17:39
To: 'Martin Čech'; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] wrong validation message in toolshed
Hi Martin,
Thanks. I fixed the problems in the .xml files, now referring to “../match_library.py” .
Now the error I get when I try to reset the repository metadata is 502:
502 Bad Gateway
nginx/1.2.1
Regards,
Pieter
From: Martin Čech [mailto:marten@bx.psu.edu]
Sent: donderdag 19 maart 2015 15:02
To: Lukasse, Pieter; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] wrong validation message in toolshed
Hi Pieter,
there seems to be either multiple incorrect links to the file or the wrappers expect multiple files that are missing from the repo. E.g. your wrapper library_lookup.xml refers to a file /GCMS/match_library.py which does not exist. (on this
line: <code file="match_library.py" />)
After you correct these links you might want to 'Reset repository metadata'.
Martin
On Thu, Mar 19, 2015 at 8:18 AM Lukasse, Pieter <pieter.lukasse@wur.nl> wrote:
Hi ,
I’m getting this error message, which is not correct since the file IS available in the repository.
Metadata may have been defined for some items in revision 'f70b775dcaa5'. Correct
the following problems if necessary and reset metadata.
create_model.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository
to correct this error.
library_lookup.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository
to correct this error.
query_metexp.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository
to correct this error.
query_mass_repos.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository
to correct this error.
metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the
repository to correct this error.
rankfilterGCMS_tabular.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the
repository to correct this error.
metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the
repository to correct this error.
I installed the package anyway and it works, which proves there is no real problem.
See
https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_metabolomics2
Regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Department of Bioinformatics (Bioscience)
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
T: +31-317481122;
M: +31-628189540;
skype: pieter.lukasse.wur
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