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
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
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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