Hi JanakiRam,
galaxy-dist is the stable version of Galaxy and galaxy-central is the
development version. But you can also track galaxy-central and the
stable branch as I do. Galaxy-central [stable] should be the same as
galaxy-dist in theory. In practise galaxy-central [stable] get more
fixes during a development window.
Galaxy is released ~ every 2 month and the next release will happen in
the next 1-2 weeks I think. Galaxy-central (stable-next) ist already
branched.
Cheers,
Bjoern
Am 04.04.2014 07:56, schrieb Janaki Rama Rao Gollapudi:
Hi Greg/Bjoern,
Thanks for all your help. I checkout the galaxy-central code
base(previously I am using galaxy-dist code base) and uploaded my custom
tool(with both tool and repository dependency) in to toolshed and also
installed custom tool from galaxy. The dependency tool also installed
successfully.
I have few doubts:
- When are you planning to merge these changes into galaxy-dist ?
- As mentioned in the galaxy
wiki<https://wiki.galaxyproject.org/Admin/GetGalaxy> we
are using galaxy-dist code base. Can we use galaxy-central ?
- What is the difference between galaxy-dist and galaxy-central ?
Thanks,
JanakiRam
On Thu, Apr 3, 2014 at 7:54 PM, Björn Grüning <bjoern.gruening(a)gmail.com>wrote:
> Hi,
>
> thanks for fixing it Greg. Would it also be possible to get a more
> concrete error message in such cases where the repository_dependencies.xml
> file is somehow broken?
>
> Thanks,
> Bjoern
>
> Am 03.04.2014 16:22, schrieb Greg Von Kuster:
>
> I should have handled the import in the same commit, but did so in the
>> following changeset. It will eliminate the problematic
>> prior_installation_required="False" attribute from the
<repository> tag
>> when a capsule is being imported.
>>
>> changeset: 12944:59bd7349a128
>> tag: tip
>> user: greg
>> date: Thu Apr 03 10:19:46 2014 -0400
>> summary: Upon import, handle problematic prior_installation_required
>> attribute incorrectly added (and set to "False") to the
<repository> tag
>> when a repository was exported.
>>
>> Greg Von Kuster
>>
>> On Apr 3, 2014, at 9:53 AM, Janaki Rama Rao Gollapudi <
>> janakiram.gollapudi(a)india.semanticbits.com> wrote:
>>
>> Thanks Greg, I will verify with new changes.
>>>
>>>
>>> Thanks,
>>> JanakiRam
>>>
>>>
>>> On Thu, Apr 3, 2014 at 7:05 PM, Greg Von Kuster <greg(a)bx.psu.edu>
wrote:
>>> Hello Janaki and Björn,
>>>
>>> This problematic behavior is a result of a bug in the repository export
>>> process which has been fixed in the following changeset which is currently
>>> available in the Galaxy central repo. Thanks very much for reporting this.
>>>
>>>
https://bitbucket.org/galaxy/galaxy-central/commits/
>>> 773578e65580e3488fadc144739d82f86d9b30f3
>>>
>>> Greg Von Kuster
>>>
>>> On Apr 3, 2014, at 7:53 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
>>>
>>> Yes, if that is the behavior, that is definitely a bug. I'll take a
>>>> look and get back to you on this.
>>>>
>>>> Thanks!
>>>>
>>>> On Apr 3, 2014, at 7:35 AM, Björn Grüning
<bjoern.gruening(a)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.gruening(a)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.gruening(a)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.gollapudi(a)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.gruening(a)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.gollapudi(a)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/
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>> ___________________________________________________________
>>>>> 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:
>>>>>
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>>>>>
>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>
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>>>>>
>>>>>
>>>>
>>>> ___________________________________________________________
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>>>>
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>>>>
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>>>>
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>>>>
>>>>
>>>
>>> ___________________________________________________________
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>>
>>
>>
>>
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