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@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/

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@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@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@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/

Hi Bjoern, Please see my comments inline. On Thu, Apr 3, 2014 at 3:14 PM, Björn Grüning <bjoern.gruening@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@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@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@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/

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@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@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@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@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@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/ > > > >

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.gruening@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@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@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@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@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@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/ >>> >>> >>> >>> >>> >

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/773578e65580e3488fadc144... Greg Von Kuster On Apr 3, 2014, at 7:53 AM, Greg Von Kuster <greg@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@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@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@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@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@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@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: 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/

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@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@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/773578e65580e3488fadc144...

Greg Von Kuster

On Apr 3, 2014, at 7:53 AM, Greg Von Kuster <greg@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@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@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@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@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@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@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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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@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@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@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@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@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@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@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@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@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@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: http://lists.bx.psu.edu/

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Hello Björn, I've enhanced the error message displayed in 12959:64d677b1e16a, which is available in the next-stable branch, so it will be included in the upcoming release. This message is tricky, because it is only displayed when visiting the Tool Shed from Galaxy to install a repository that has an invalid repository dependency definition. This scenario does not provide the context for the precise cause of the invalid definition. Visiting the Tool Shed directlry (not from Galaxy) and dispaying the repositoryu should provide a more detailed message regarding the problem. Thanks! Greg Von Kuster On Apr 3, 2014, at 10:24 AM, Björn Grüning <bjoern.gruening@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@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@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/773578e65580e3488fadc144...

Greg Von Kuster

On Apr 3, 2014, at 7:53 AM, Greg Von Kuster <greg@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@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@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@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@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@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@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: http://lists.bx.psu.edu/

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