I installed a local galaxy on Centos 6 and I followed the instructions on how 
to install samtools/bwa/bowtie found here 

I setup the correct env. for these programs correctly.  Since I have no issues 
with the bwa and bowtie so I assumed I got everything correctly but that was 
not true since I keep getting the following error when I try Sam-To-Bam...
galaxy.jobs.runners.local DEBUG 2013-02-05 10:37:36,053 execution of external 
set_meta for job 62 finished
galaxy.jobs DEBUG 2013-02-05 10:37:36,070 Tool did not define exit code or 
stdio handling; checking stderr for success
galaxy.datatypes.metadata DEBUG 2013-02-05 10:37:36,101 setting metadata 
externally failed for HistoryDatasetAssociation 76: Error Setting BAM Metadata: 
/bin/sh: samtools: command not found
galaxy.jobs.runners.local ERROR 2013-02-05 10:37:36,134 Job wrapper finish 
method failed
Traceback (most recent call last):
  File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 
156, in run_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 412, 
in finish
    dataset.datatype.set_meta( dataset, overwrite = False ) #call 
datatype.set_meta directly for the initial set_meta call during dataset creation
  File "/usr/local/galaxy/galaxy-dist/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
galaxy.datatypes.metadata DEBUG 2013-02-05 10:37:36,239 Cleaning up external 
metadata files

*         Samtools is in the path:  >echo $PATH

*         I setup the env.sh as recommended. >more 
#Configure PATH to Samtools binaries
export PATH

*         And here what I have in the bin:> ls -lh 
total 1.5M
-rwxr-xr-x 1 galaxy galaxy 2.4K Jan 29 12:53 blast2sam.pl
-rwxr-xr-x 1 galaxy galaxy 2.1K Jan 29 12:53 bowtie2sam.pl
-rwxr-xr-x 1 galaxy galaxy  19K Jan 29 12:53 export2sam.pl
-rwxr-xr-x 1 galaxy galaxy 4.9K Jan 29 12:53 interpolate_sam.pl
-rwxr-xr-x 1 galaxy galaxy 5.9K Jan 29 12:53 novo2sam.pl
-rwxr-xr-x 1 galaxy galaxy 2.0K Jan 29 12:53 psl2sam.pl
-rwxr-xr-x 1 galaxy galaxy 7.7K Jan 29 12:53 sam2vcf.pl
-rwxrwxr-x 1 galaxy galaxy 1.4M Jan 29 12:53 samtools
-rwxr-xr-x 1 galaxy galaxy  14K Jan 29 12:53 samtools.pl
-rwxr-xr-x 1 galaxy galaxy 2.7K Jan 29 12:53 soap2sam.pl
-rwxr-xr-x 1 galaxy galaxy 2.7K Jan 29 12:53 wgsim_eval.pl
-rwxr-xr-x 1 galaxy galaxy 2.4K Jan 29 12:53 zoom2sam.pl

*         I could ran the samtools from anywhere in the system including from 
"galaxy" account.

*         I looked at this thread which the guy has similar problem but he was 
trying to set it up in a cluster and installing it on Ubunto.  I read the whole 
thing and tried everything in there but no luck....


*         I have installed R and Python/rpy and set their env. as required (I 
THINK) assuming this might be a cause but I do not see anything in the error 
log that will indicate that...

Can anyone help in debugging this issue please?



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