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

--

Central Veterinary Institute of Wageningen UR (CVI)
Department of Infection Biology
PO box 65, 8200 AB Lelystad, NL
Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
 
Tel:  +31-(0)320-293391
Fax: +31-(0)320-238153
E-mail: eric.kuijt@wur.nl
Web: http://www.cvi.wur.nl

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/