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.

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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