On Tue, Feb 24, 2015 at 9:19 AM, Björn Grüning
<bjoern.gruen...@gmail.com> wrote:
> Am 24.02.2015 um 10:03 schrieb Peter Cock:
>> ... So far so good, but at that point Galaxy
>> tries to index the BAM file itself. This happens for any BAM file,
>> regardless of the tool which created it - and simply expects samtools
>> on the $PATH.
>>
>> If this is on the wiki (core dependencies of Galaxy itself), could
>> someone post the URL here please?
>
> It is not listed here:
> https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList

Yes, that page is about dependencies of add-on tools (things
that existing or new tools may assume are installed).

In this case samtools is expected by the Galaxy core (not a tool).
What else falls into this set of dependencies?

> I can be wrong but I think Galaxy will search in
> <galaxy-tools>/samtools/default if samtools is not on your $PATH.
>
> Can anyone confirm this?
>
> Ciao,
> Bjoern

I don't know, sorry.

Peter
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