Hi, Bjoern, Yes the summary looks correct.
Greg, I have added tool_dependencies.xml to the same custom tool and installed it successfully in my local galaxy. But If I add repository_dependencies.xml to my custom tool and try to install the tool, then galaxy showing an error message that the dependency xml file is invalid. Thanks, JanakiRam On Thu, Apr 3, 2014 at 5:05 PM, Björn Grüning <bjoern.gruen...@gmail.com>wrote: > Hi JanakiRam, > > I will take Greg into CC. He is the main Tool Shed developer, maybe we > spotted a bug in populating "prior_installation_required" in > repository_dependencies.xml file. He probably knows if that is supposed to > work. > > Greg, to summarize our findings. It seems that if JanakiRam uploads a > repository_dependencies.xml file into a local toolshed the > "prior_installation_required='False'" will be inserted. If he tries to > install it, Galaxy complains about a wrong syntax inside the > repository_dependecies.xml file. Imho "prior_installation_required" does > not make sense in repository_dependencies.xml or? Is that an bug? > > JanakiRam can you confirm my summary? > > Thanks, > Bjoern > > Am 03.04.2014 12:49, schrieb Janaki Rama Rao Gollapudi: > >> Hi, >> >> I am using latest checkout from >> https://bitbucket.org/galaxy/galaxy-dist/(Just now I also updated my >> >> local galaxy code base). Yes, without >> repository dependency everything working fine. >> >> Thanks, >> JanakiRam >> >> >> >> On Thu, Apr 3, 2014 at 3:39 PM, Björn Grüning <bjoern.gruen...@gmail.com> >> wrote: >> >> Hi, >>> >>> I just tested it in the test-toolshed and for me >>> 'prior_installation_required' is not inserted. Which Galaxy version do >>> you >>> use? Please note, that I'm not sure if that is really causing the trouble >>> you have seen. >>> If you remove the repository dependency everything is working as >>> expected? >>> >>> >>> >>> Am 03.04.2014 12:01, schrieb Janaki Rama Rao Gollapudi: >>> >>> Hi Bjoern, >>> >>>> >>>> Please see my comments inline. >>>> >>>> On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning < >>>> bjoern.gruen...@gmail.com> >>>> wrote: >>>> >>>> Hi Janaki, >>>> >>>>> >>>>> can you try to remove this prior_installation_required completely? >>>>> >>>>> >>>>> I didn't added 'prior_installation_required' in the >>>> repository_dependencies.xml(as this is optional), it got added when I >>>> exported repository files from tool shed. Actual >>>> repository_dependencies.xml file has below content. >>>> >>>> <?xml version="1.0"?> >>>> <repositories description="test description"> >>>> <repository name="string_occurrence" owner="janakiram-t1" /> >>>> </repositories> >>>> >>>> >>>> Also why do you need a repository dependency, I think that is not >>>> needed >>>> >>>>> or? >>>>> >>>>> >>>>> This is the first time I working with repository >>>> dependencies, >>>> so >>>> for testing I am trying to add simple repository dependency to my custom >>>> tool. >>>> >>>> >>>> Cheers, >>>>> Bjoern >>>>> >>>>> Am 03.04.2014 09:30, schrieb Janaki Rama Rao Gollapudi: >>>>> >>>>> Hi Bjoern, >>>>> >>>>> >>>>>> I also exported both the repositories from local toolshed. Please find >>>>>> the >>>>>> attached files. >>>>>> >>>>>> >>>>>> Thanks, >>>>>> JanakiRam >>>>>> >>>>>> >>>>>> On Thu, Apr 3, 2014 at 12:50 PM, Janaki Rama Rao Gollapudi < >>>>>> janakiram.gollap...@india.semanticbits.com> wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> >>>>>>> Thanks for quick reply. Please find the attached .tar file of both >>>>>>> the >>>>>>> repositories. >>>>>>> >>>>>>> >>>>>>> Thanks, >>>>>>> JanakiRam >>>>>>> >>>>>>> >>>>>>> On Thu, Apr 3, 2014 at 12:45 PM, Björn Grüning < >>>>>>> bjoern.gruen...@gmail.com>wrote: >>>>>>> >>>>>>> This all seems to be fine, can you send me a tarball with both >>>>>>> >>>>>>> repositories ... >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Bjoern >>>>>>>> >>>>>>>> Am 03.04.2014 09:05, schrieb Janaki Rama Rao Gollapudi: >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> >>>>>>>>> Did anyone faced this issue ?. I struck here. Please suggest me. >>>>>>>>> >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> JanakiRam >>>>>>>>> >>>>>>>>> >>>>>>>>> On Wed, Apr 2, 2014 at 3:10 PM, Janaki Rama Rao Gollapudi < >>>>>>>>> janakiram.gollap...@india.semanticbits.com> wrote: >>>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> >>>>>>>>> I have implemented a custom tool called 'barcode-parse' and >>>>>>>>>> uploaded >>>>>>>>>> this >>>>>>>>>> custom to into my local tool shed(which is running at >>>>>>>>>> http://localhost:9009). Also able to install this custom tool >>>>>>>>>> from >>>>>>>>>> galaxy. >>>>>>>>>> >>>>>>>>>> Then I have added simple repository dependency. I have created a >>>>>>>>>> xml >>>>>>>>>> file >>>>>>>>>> 'repository_dependencies.xml'. Then I created a new repository in >>>>>>>>>> the >>>>>>>>>> toolShed called 'Test' and uploaded all necessary files(.py, >>>>>>>>>> definition >>>>>>>>>> xml >>>>>>>>>> file and repository dependency xml file) into this repository. (I >>>>>>>>>> have >>>>>>>>>> created another repository called 'string_occurrence' and uploaded >>>>>>>>>> necessary files into toolShed which is used as dependency >>>>>>>>>> repository) >>>>>>>>>> >>>>>>>>>> <?xml version="1.0"?> >>>>>>>>>> <repositories description=""> >>>>>>>>>> <repository toolshed="http://localhost:9009"; >>>>>>>>>> name="string_occurrence" owner="janakiram-t1" /> >>>>>>>>>> </repositories> >>>>>>>>>> >>>>>>>>>> I tried to install custom tool 'barcode-parse' from galaxy, but I >>>>>>>>>> got >>>>>>>>>> below error message. >>>>>>>>>> >>>>>>>>>> The repository dependency definitions for this repository are >>>>>>>>>> invalid >>>>>>>>>> and >>>>>>>>>> will be ignored. >>>>>>>>>> >>>>>>>>>> I followed the steps mentioned in the galaxy wiki<https://wiki. >>>>>>>>>> galaxyproject.org/SimpleRepositoryDependencies> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Am I doing anything wrong? Please suggest me on this. >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> JanakiRam >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ___________________________________________________________ >>>>>>>>> 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/ >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>> >>>>>> >>>> >>
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