Dave, Thank you very much, it worked indeed. The gz export does not work yet, but this is apparently now due to a problem with mercurial (An error occurred while processing your request: - Archive type not allowed: gz). Anyway, this is not a main issue and we are going to be able to focus on the tools, without apache.
Thank thank thank Chris Christophe Antoniewski <http://sciencesenmarche.org/> Drosophila Genetics and Epigenetics Laboratoire de Biologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 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/ 2014-09-11 15:18 GMT+02:00 Dave Bouvier <d...@bx.psu.edu>: > 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/
