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.gollap...@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 <g...@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 <g...@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.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





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