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.gruen...@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.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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___________________________________________________________
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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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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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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:
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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