great, thanks
On 26 November 2014 at 16:39, bjoern.gruen...@googlemail.com
bjoern.gruen...@gmail.com wrote:
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 iseegl...@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.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
--
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Department of Infection Biology
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Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
Tel: +31-(0)320-293391
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