Hi Jen,
Thank you for your quick response.
I changed the env.sh file to what you seggested, and the problem still existed.
I am pasting more details below:
I submitted a job to convert sam to bam, and the job was running forever
without outputing the result. I then checked the log, and it read:
Traceback (most recent call last):
File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line
336, in finish_job
drm_job_state.job_wrapper.finish( stdout, stderr )
File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/__init__.py", line 637, in
finish
dataset.set_meta( overwrite = False )
File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/model/__init__.py", line 875,
in set_meta
return self.datatype.set_meta( self, **kwd )
File "/mnt/galaxyTools/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
It means that the samtools is not in the PATH. I tried to set the PATH in a
couple of methods according the Galaxy documentation:
1. put the path in the env.sh in the tool directory and symbolink default to
the tool directory, e.g. default -> =/mnt/galaxyTools/tools/samtools/0.1.18
2. put -v PATH=/mnt/galaxyTools/tools/samtools/0.1.18 in ~/.sge_request
3. put -v PATH=/mnt/galaxyTools/tools/samtools/0.1.18 in /path/sge_request
none of them worked, and I got the above same problem.
Then I checked the job log file in the job_working_directory, and it read:
Samtools Version: 0.1.18 (r982:295)
SAM file converted to BAM
which shows that sge knows the PATH of samtools. To double check it, I added
samtools index to Galaxy, and it worked well. I am very confused why SGE knows
the tool path but cannot run the job correctly.
The system I am using is ubuntu on EC2 (the image id is: ami-999d49f0, which is
the one used by StarCluster). I checked out the code from galaxy-dist on
bitbucket. Other tools such as bwa and bowtie worked well using the same
setting method(put env.sh in the tools directory to set the tool path)
Thanks you very much,
Cai
--- 12年4月18日，周三, Jennifer Jackson <j...@bx.psu.edu> 写道：
> 发件人: Jennifer Jackson <j...@bx.psu.edu>
> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh:
> samtools: not found
> 收件人: "zhengqiu cai" <caizhq2...@yahoo.com.cn>
> 抄送: galaxy-dev@lists.bx.psu.edu
> 日期: 2012年4月18日,周三,上午2:12
> 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
> >
> >
> ___________________________________________________________
> > Please keep all replies on the list by using "reply
> all"
> > in your mail client. To manage your subscriptions
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> > and other Galaxy lists, please use the interface at:
> >
> > http://lists.bx.psu.edu/
>
> --
> Jennifer Jackson
> http://galaxyproject.org
>
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