Hi Aaron,

I am just following up with a note that this has been fully resolved.
Please let us know if you find any more problems.

Thank you for using Galaxy.

Martin

On Wed, Aug 12, 2015 at 7:21 PM Aaron Petkau <aaron.pet...@gmail.com> wrote:

> Heh, always something that's discovered after the fact.  Happens to me all
> the time.  Thanks for getting back to me quickly.  Looks like the fix you
> did works.  Only other tool is sam_to_bam
> https://toolshed.g2.bx.psu.edu/repository?repository_id=01221a8c57f0fc1a&changeset_revision=c73bf16b45df.
> Hopefully not too much trouble.
>
> Thanks again Martin,
>
> Aaron
> On Wed, Aug 12, 2015 at 5:10 PM, Martin Čech <mar...@bx.psu.edu> wrote:
>
>> Hi Aaron,
>>
>> this is most probably connected with a bug that we discovered today in
>> the 'reset metadata for all my repositories' feature. Unfortunately we
>> discovered it by running it on Main Tool Shed. We have an alternate (time
>> consuming) way of fixing individual repos (like I just did for the
>> samtools_mpileup) so if you give me a list of tools you need to use with
>> old revisions I will make sure they are in a good shape.
>>
>> This only affects devteam repos.
>> We are working on a fix, please bare with us.
>>
>> Thank you for using Galaxy!
>>
>> Martin
>>
>> On Wed, Aug 12, 2015 at 5:44 PM Aaron Petkau <aaron.pet...@gmail.com>
>> wrote:
>>
>>> Hey everyone,
>>>
>>> So I rely a lot on specific versions of tools in the toolshed, and am
>>> often testing out the install process to make sure everything's working.
>>> Today I noticed that my install process was failing, and it looks like it's
>>> due to not being able to install previous versions of tools through the
>>> API.  It seems to default to installing the latest version of a tool.
>>>
>>> For example, for the tool samtools_mpileup
>>> <https://toolshed.g2.bx.psu.edu/repository?repository_id=01d08a1b766b864e&changeset_revision=aa0ef6f0ee89>,
>>> if I run the code:
>>>
>>> gi.toolShed.install_repository_revision("http://toolshed.g2.bx.psu.edu/
>>> ",'samtools_mpileup','devteam','973fea5b4bdf',install_tool_dependencies=True,install_repository_dependencies=True)
>>>
>>> in bioblend (to install revision 973fea5b4bdf) I instead get the latest
>>> (aa0ef6f0ee89) revision installed.  I can see the previous revision still
>>> exists
>>> https://toolshed.g2.bx.psu.edu/repository?repository_id=01d08a1b766b864e&changeset_revision=973fea5b4bdf
>>> .
>>>
>>> I'm wondering if something has changed here?  I remember being able to
>>> install old versions of tools through the API before, but maybe I'm getting
>>> mixed up?
>>>
>>> Thanks,
>>>
>>> Aaron
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