is bash_profile the best place for this, or is somewhere else better? Cheers Anna
On 26 November 2014 at 16:29, bjoern.gruen...@googlemail.com < bjoern.gruen...@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 <iseegl...@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.ku...@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 <iseegl...@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.ku...@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/ >> > >
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