Hi Bjoern,

Thanks for the note, and sorry I could not type your name in the original
alphabet -- it looks Icelandic. :-)

I'll follow your instructions and see how it goes.

Best,
Rui

On Fri, Mar 7, 2014 at 7:17 PM, Björn Grüning <bjoern.gruen...@gmail.com>wrote:

> Hi Rui,
>
> if you want to use only the local installation and not the toolshed one,
> go to the toolshed installation inside your galaxy and remove under "manage
> tool dependencies" the dependency on macs2. As soon as you get rid of the
> dependency the local installation is used.
>
> Cheers,
> Bjoern
>
> P.S. There is also a MACS2 version now for testing
>
> Am 08.03.2014 00:48, schrieb ruiwang.sz:
>
>> Hi Guys,
>>
>> I'm sorry to post multiple times for the same question. Now I removed all
>> the specifics of my problem and I only want someone to point me to the
>> right documentation. Admins, I know you are busy, but don't you want more
>> people to benefit from this platform?
>>
>> When galaxy upgraded it started using the tool_shed version of the tool
>> and
>> killed the tools we installed ourselves. Right now we have both versions.
>> How should we manage this situation properly if we don't want the
>> tool_shed
>> version and want to keep using what we had before?
>>
>> Nate said that MACS came with galaxy before. I didn't know that. From the
>> day we started using MACS it was installed by ourselves. Not sure if that
>> caused the problem.
>>
>> Thanks,
>> Rui
>>
>>
>>
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