Hi All,

I was trying to setup the Galaxy tool dependencies, and I met the following 
problem when running sam-to-bam in samtools:
Traceback (most recent call last):
  File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", 
line 336, in finish_job
    drm_job_state.job_wrapper.finish( stdout, stderr )
  File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/__init__.py", line 
637, in finish
    dataset.set_meta( overwrite = False )
  File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/model/__init__.py", line 
875, in set_meta
    return self.datatype.set_meta( self, **kwd )
  File "/mnt/galaxyTools/cai_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

I already set the path of samtools
Below I pasted how I set the path:
ubuntu@master:/mnt/galaxyTools/tools/samtools$ ll
total 8
drwxr-xr-x  4 ubuntu ubuntu   65 2012-04-16 19:09 ./
drwxr-xr-x 38 ubuntu ubuntu 4096 2012-04-16 18:41 ../
drwxr-xr-x  2 ubuntu ubuntu   53 2012-04-16 19:08 0.1.12/
drwxr-xr-x  2 ubuntu ubuntu   53 2012-04-13 20:23 0.1.7/
lrwxrwxrwx  1 ubuntu ubuntu   38 2012-04-16 19:09 default -> 

ubuntu@master:/mnt/galaxyTools/tools/samtools$ more default/env.sh

I used the same way to set other programs, such as bwa and bowtie, and they 
worked perfectly. Only samtools could not work.
I even used the full path of samtools in the wrapper file sam_to_bam.py, and it 
was not working neither.

I am wondering if any one met the same problem, or some one can give me some 

Thank you very much.


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