Dear all,
with older Galaxies (prior to latest_15.03 I think), you could satisfy Galaxy's samtools dependence for indexing bam files by having a samtools executable in tool-dependencies/samtools/default/bin (with the tool-dependencies directory declared as tool_dependency_dir in galaxy.ini of course).
Now (checked with latest_15.03 and .05), this is not working any more! The executable will still be used during bam uploads, but not when a bam file gets created by a tool.
The reason is that before the job runner (tested this with the local job runner only) used to build the dependency shell command for dependency 'samtools' before finishing a job, but now the job wrapper finish method fails because it naively expects to find samtools on $PATH.
Best, Wolfgang