Christophe,

Unfortunately, exporting a capsule without a proxy in front of the tool shed will fail to find dependencies if the dependencies were defined with the proxy in place. One solution would be to re-upload the dependency definitions without using the proxy, leaving the changeset_revision and toolshed attributes undefined. This will make the tool shed recalculate tool shed URLs and changeset revisions for the dependency relationships, and the capsule export should then find them.


   --Dave B.

On 09/10/2014 12:11 PM, Christophe Antoniewski wrote:

I am replying to myself to report limited progresses... :

if we run the tool shed server without apache, the "export capsule" job
works, except that the repository dependencies are not seen (no "Export
repository dependencies?" checkbox to check). Without this new layer of
complication, we would leave apache which is not really required for
tool development in our local toolshed. But "Export repository
dependencies" matters...

Sure we are missing something around Apache and tool_shed_wsgi.ini
configuration, but still lost..

Chris


Christophe Antoniewski


Drosophila Genetics and Epigenetics
Laboratoire de Biologie du Développement
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05
christophe.antoniew...@upmc.fr <mailto:christophe.antoniew...@upmc.fr>
http://bio-dev.snv.jussieu.fr/

Tel +33 1 44 27 34 39
Fax+33 1 44 27 34 45
Mobile+33 6 68 60 51 50

http://drosophile.org

http://www.sciencesenmarche.org/


2014-09-08 19:24 GMT+02:00 Christophe Antoniewski
<christophe.antoniew...@snv.jussieu.fr
<mailto:christophe.antoniew...@snv.jussieu.fr>>:

    Hi,

    Here is a question maybe to Greg:

    Since the GCC2014 we started a local toolshed following the
    instructions in
    http://gregvonkuster.org/galaxy-tool-shed-framework-building-galaxy-tools/

    It works nicely, except that today I tried to export repository
    capsules ("export this revision") from the local toolshed and it
    returns the following error (see below). I cannot remember whether I
    had ever tested this particular action since the local tool shed set
    up. Thus I even cannot say whether the bug is due to an original
    misconfiguration or it happened later on.

    I can add that the local toolshed is served by apache with rewriting
    rules (I am saying this because in addition it is not possible to
    download repositories as gz archives etc... and suspect that there
    is maybe a problem, in addition, with the apache config).

    Any help appreciated !

    Regards

    Christophe

    ---------------

    URL:
    
http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f
    Module galaxy.web.framework.middleware.error:*149* in |__call__|
    |>>
    
<http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>app_iter
    *=* self*.*application*(*environ*,* sr_checker*)*|
    Module paste.debug.prints:*106* in |__call__|
    |>>
    
<http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>environ*,*
    self*.*app*)*|
    Module paste.wsgilib:*543* in |intercept_output|
    |>>
    
<http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>app_iter
    *=* application*(*environ*,* replacement_start_response*)*|
    Module paste.recursive:*84* in |__call__|
    |>>
    
<http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>*return*
    self*.*application*(*environ*,* start_response*)*|
    Module paste.httpexceptions:*633* in |__call__|
    |>>
    
<http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>*return*
    self*.*application*(*environ*,* start_response*)*|
    Module galaxy.web.framework.base:*132* in |__call__|
    |>>
    
<http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>*return*
    self*.*handle_request*(* environ*,* start_response *)*|
    Module galaxy.web.framework.base:*190* in |handle_request|
    |>>
    
<http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>body
    *=* method*(* trans*,* ****kwargs *)*|
    Module galaxy.webapps.tool_shed.controllers.repository:*1249* in
    |export|
    |>>
    
<http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>repositories_archive_filename
    *=* os*.*path*.*basename*(* repositories_archive*.*name *)*|
    *AttributeError: 'NoneType' object has no attribute 'name'*


    Christophe Antoniewski


    Drosophila Genetics and Epigenetics
    Laboratoire de Biologie du Développement
    9, Quai St Bernard, Boîte courrier 24
    75252 Paris Cedex 05
    christophe.antoniew...@upmc.fr <mailto:christophe.antoniew...@upmc.fr>
    http://bio-dev.snv.jussieu.fr/

    Tel +33 1 44 27 34 39 <tel:%2B33%201%2044%2027%2034%2039>
    Fax+33 1 44 27 34 45 <tel:%2B33%201%2044%2027%2034%2045>
    Mobile+33 6 68 60 51 50 <tel:%2B33%206%2068%2060%2051%2050>

    http://drosophile.org

    http://www.sciencesenmarche.org/




___________________________________________________________
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:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/

___________________________________________________________
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:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Reply via email to