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.antoniewski@upmc.fr <mailto:christophe.antoniewski@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://www.sciencesenmarche.org/
2014-09-08 19:24 GMT+02:00 Christophe Antoniewski <christophe.antoniewski@snv.jussieu.fr <mailto:christophe.antoniewski@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.antoniewski@upmc.fr <mailto:christophe.antoniewski@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://www.sciencesenmarche.org/
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