Hi,
I installed a local galaxy on Centos 6 and I followed the instructions on how to install samtools/bwa/bowtie found here http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup.
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 $PATH /usr/local/galaxy/galaxy_env/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/java/latest/bin:/usr/local/scripts:/usr/local/galaxy/software/samtools/0.1.16/bin/:/usr/local/galaxy/software/bwa/0.2.6/bin/:/usr/local/galaxy/software/bowtie/0.12.7/bin/:/usr/local/galaxy/software/fastx/0.0.13/bin/:/usr/local/galaxy/software/ncbi-blast/2.2.27/bin/:/usr/local/galaxy/software/lastz-distrib/1.02.00/bin/
* I setup the env.sh as recommended. >more //usr/local/galaxy/software/samtools/0.1.16/env.sh #Configure PATH to Samtools binaries PATH="/usr/local/galaxy/software/samtools/0.1.16/bin/:$PATH" export PATH
* And here what I have in the bin:> ls -lh /usr/local/galaxy/software/samtools/0.1.16/bin/ 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....
http://gmod.827538.n3.nabble.com/Exception-Error-Setting-BAM-Metadata-bin-sh...
* 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?
Thanks
hakeem