Hi Cai,

Please double check that your env.sh file contains the following:


    PATH="/mnt/galaxyTools/tools/samtools/0.1.12:$PATH"
    export PATH


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


Hopefully this helps,

Jen
Galaxy team

On 4/16/12 12:43 PM, zhengqiu cai wrote:
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 ->  
/mnt/galaxyTools/tools/samtools/0.1.12/

ubuntu@master:/mnt/galaxyTools/tools/samtools$ more default/env.sh
PATH=/mnt/galaxyTools/tools/samtools/0.1.12:$PATH

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 
hints.

Thank you very much.

Cai

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