On Apr 24, 2012, at 8:36 PM, Michael Moore wrote:

> There is apparently a persistent problem with samtools which normally lives at /usr/bin/samtools.  I encountered a similar problem in Python when uploading BAM files.
>
> I did not resolve the problem.  I hacked for a while on binary.py in a lib/ subdirectory and used os.system to send myself mail describing the effective path at various points, and I added a missing
>
> logging.basicConfig()
>
> statement and scattered some log.WARNING statements strategically.  All this told me nothing.  So I made a few symlinks to samtools.  The one that got things working was
>
> ln -s /usr/bin/samtools /home/galaxy/bin/samtools
>
> so--worked around but not resolved.

Hi Michael,

For tools that output BAM, samtools needs to be in your $PATH, or has to be set up via the tool dependencies system.  See the following for details:

   http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies

For SGE, you can modify the $PATH used on the cluster in ~/.sge_request or the file specified in the 'environment_setup_file' galaxy config option.

--nate

>
> Michael
>
> On Tue, Apr 17, 2012 at 12:15 PM, zhengqiu cai <caizhq2005@yahoo.com.cn> wrote:
> Hi All,
>
> I submitted a job to convert sam to bam, and the job was running forever without outputing the result. I then checked the log, and it read:
> Traceback (most recent call last):
>  File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 336, in finish_job
>    drm_job_state.job_wrapper.finish( stdout, stderr )
>  File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/__init__.py", line 637, in finish
>    dataset.set_meta( overwrite = False )
>  File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/model/__init__.py", line 875, in set_meta
>    return self.datatype.set_meta( self, **kwd )
>  File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/datatypes/binary.py", line 179, in set_meta
>    raise Exception, "Error Setting BAM Metadata: %s" % stderr
> Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found
>
> It means that the samtools is not in the PATH. I tried to set the PATH in a couple of methods according the Galaxy documentation:
> 1. put the path in the env.sh in the tool directory and symbolink default to the tool directory, e.g. default -> =/mnt/galaxyTools/tools/samtools/0.1.18
> 2. put -v PATH=/mnt/galaxyTools/tools/samtools/0.1.18 in ~/.sge_request
> 3. put -v PATH=/mnt/galaxyTools/tools/samtools/0.1.18 in /path/sge_request
>
> none of them worked, and I got the above same problem.
>
> Then I checked the job log file in the job_working_directory, and it read:
> Samtools Version: 0.1.18 (r982:295)
> SAM file converted to BAM
>
> which shows that sge knows the PATH of samtools. To double check it, I added samtools index to Galaxy, and it worked well. I am very confused why SGE knows the tool path but cannot run the job correctly.
>
> The system I am using is ubuntu on EC2. I checked out the code from galaxy-dist on bitbucket. Other tools such as bwa and bowtie worked well using the same setting method(put env.sh in the tools directory to set the tool path)
>
> Thank you very much for any help or hints.
>
> Cai
>
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