Il 24.02.2015 10:19 Björn Grüning ha scritto:

Am 24.02.2015 um 10:03 schrieb Peter Cock:

On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon wrote:

The main problem for me was that I was not aware that the tophat tool
had a dependency on a command line tool outside of galaxy
installation. I see in the admin interface that tophat has a
dependency on samtools of type package and I assumed that should
provide the samtools binary. Of course I have not read the manuals
regarding tool sheds, dependencies, etc so thats probably where my
problem started in the first place...
I can see your chain of thought here. Unfortunately while the tophat
tool (or any tool) may explicitly use samtools (and request a
particular version via the dependencies system), once the tool has
finished it has produced a BAM file. 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:

I can be wrong but I think Galaxy will search in/samtools/default if
samtools is not on your $PATH.

Can anyone confirm this?

Galaxy should search first in <tool_dependencies_dir>/samtools/default/ (where <tool_dependencies_dir> is what you have configured in the tool_dependency_dir directive of config/galaxy.ini), then in $PATH .


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