I would use .bashrc. You can also try to symlib the default dir to the actual /bin directory. Maybe this works for you.

2014-11-26 17:36 GMT+01:00 Anna Terry <iseeglass@googlemail.com>:

is bash_profile the best place for this, or is somewhere else better?

Cheers
Anna

On 26 November 2014 at 16:29, bjoern.gruening@googlemail.com <bjoern.gruening@gmail.com> wrote:

The problem is that bowtie and Galaxy (can) use a different samtools version. Galaxy needs samtools to create metadata for BAM files, so this process is actually running ofter bowtie has finished.

You need a samtools version globally accessible for Galaxy. Make sure you have smatools in your $PATH and than restart Galaxy.

Cheers,

Bjoern

2014-11-26 17:14 GMT+01:00 Anna Terry <iseeglass@googlemail.com>:

I just tried still the same problem.

I ran bowtie2 to test, again I saw samtools come up on top, but same 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 998, 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 251, in set_meta
    raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found

On 26 November 2014 at 16:01, Eric Kuyt <eric.kuijt@wur.nl> wrote:

​Could you try going to Admin -> Manage Installed tool shed repositories

uninstall -> reinstall ​package_samtools_0_1_18

On 26 November 2014 at 16:55, Anna Terry <iseeglass@googlemail.com> wrote:

yway, I am also getting the problem with samtools filter sam or bam

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