On Nov 19, 2012, at 8:01 AM, Nicholas Tucker wrote:

> Dear all,
> I have mapped some Illumina reads to a reference using Bowtie.
> I am trying to use Sam Tools to convert Sam to Bam on our local galaxy, but 
> it always fails:
> 
> 
> Traceback (most recent call last):
>  File "/export/galaxy/galaxy-central/lib/galaxy/jobs/runners/local.py", line 
> 155, in run_job
>    job_wrapper.finish( stdout, stderr, exit_code )
>  File "/export/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py", line 396, 
> in finish
>    dataset.datatype.set_meta( dataset, overwrite = False ) #call 
> datatype.set_meta directly for the initial set_meta call during dataset 
> creation
>  File "/export/galaxy/galaxy-central/lib/galaxy/datatypes/binary.py", line 
> 213, in set_meta
>    raise Exception, "Error Setting BAM Metadata: %s" % stderr
> Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
> 
> Tool execution generated the following error message:
> 
> Unable to finish job
> 
> The resulting failure always generates a large file, as if it has almost 
> completed……
> 
> Anybody got an idea what the error might be and how to solve it please?

Hi Nick,

samtools appears to be found when running the tool itself (to convert SAM to 
BAM), however, during the setting of metadata, samtools cannot be found (to 
create the BAM index).  I'd suggest enabling 'set_metadata_externally' in the 
Galaxy config file and ensuring that the `samtools` binary is on the Galaxy 
user's $PATH when the server starts (if running jobs locally).

--nate

> 
> Thanks in advance,
> Nick
> 
> 
> 
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