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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