Cai - if you are using SGE you probably want to pass the Galaxy user's
path to the job using the
-V
switch in the system wide (or Galaxy user's home directory) sge_request file

eg I have
rlazarus@iaas1-int:~$ cat /var/lib/gridengine/default/common/sge_request
-cwd
-V

Without that switch, the job gets no path.
With -V, it inherits the job submitter's full path.

On Tue, Apr 17, 2012 at 4:26 PM, zhengqiu cai <caizhq2...@yahoo.com.cn> wrote:
> 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
>> to this
>> > and other Galaxy lists, please use the interface at:
>> >
>> >    http://lists.bx.psu.edu/
>>
>> --
>> Jennifer Jackson
>> http://galaxyproject.org
>>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/



-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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