On Tue, Feb 24, 2015 at 9:19 AM, Björn Grüning <bjoern.gruening@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