On Feb 23, 2015, at 8:23 AM, Saket Choudhary <saketkc@gmail.com> wrote:

On 22 February 2015 at 23:17, Michael Thon <mike.thon@gmail.com> wrote:
bam_index_build2() not yet

Hi Michael,

This seems to be related to this:
https://github.com/samtools/samtools/issues/199

You should probably switch to samtools 0.1.19

Saket

I figured that galaxy must be finding a samtools v1.1 even though the tool was not installed, according to the admin page. I uninstalled the samtools that was installed system-wide on the server.  Now I get this error:
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1107, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )  # call datatype.set_meta directly for the initial set_meta call during dataset creation
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 250, in set_meta
    raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
So, galaxy is not using the samtools from the installed galaxy package and is instead using the system one.  I'll try to reinstall samtools and see if that fixes it...