Hi Ross,

Thank you for your reply.
It still did not work.
I think SGE knows the path of samtools. Here is a test case I added to Galaxy, 
and it creates the index for fasta file. I pasted the samtools faidx wrapper 
and xml files below:
ubuntu@master:/mnt/galaxyTools/galaxy-dist/tools/samtools$ more 
samtools_faidx.pl
#!/usr/bin/perl
use strict;
use warnings;

if (@ARGV < 1) {
        die "Usage:     perl $0 <input fasta file>\n";
}
`samtools faidx $ARGV[0]`;
`cp ${ARGV[0]}.fai $ARGV[1]`;
exit;

ubuntu@master:/mnt/galaxyTools/galaxy-dist/tools/samtools$ more 
samtools_faidx.xml
<tool id="samtools_faidx" name="samtools faidx" version="1.0.3">
  <requirements>
    <requirement type="package">samtools</requirement>
  </requirements>
  <description>creates fasta index</description>
  <command interpreter="perl">
    samtools_faidx.pl $input1 $output1
  </command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="fasta file to be 
indexed" />
  </inputs>
  <outputs>
    <data format="fai" name="output1" label="${tool.name} on ${on_string}: 
fasta" />
  </outputs>
</tool>

It works, which shows that SGE knows the path of samtools. 


Cai

--- 12年4月18日,周三, Ross <ross.laza...@gmail.com> 写道:

> 发件人: Ross <ross.laza...@gmail.com>
> 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: "Jennifer Jackson" <j...@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu
> 日期: 2012年4月18日,周三,上午5:18
> Ah. Then you probably have a library
> path problem.
> Here's how we do it FWIW:
> 
> Assume your want your shared cluster apps in
> /data/apps/bin
> 
> To share the compiled libraries and binaries together,
> remember to
> compile apps like samtools using the
> --prefix /data/app
> flag so then you can add the /data/app/lib path to the
> galaxy user's
> path so the nodes running jobs inherit those paths because
> of the -V
> switch.
> 
> I hope this works!
> 
> 
> 
> On Tue, Apr 17, 2012 at 5:10 PM, zhengqiu cai <caizhq2...@yahoo.com.cn>
> wrote:
> > Hi Ross,
> >
> > Thank you for your reply.
> > I tried it, and it was still not working.
> > Only samtools has this problem, and the other tools
> works fine.
> >
> > samtools was compiled from source correctly. If I
> install samtools using "sudo apt-get install samtools", this
> problem is gone, but this is not a solution for since it
> does not work across the cluster.
> >
> >
> > Cai
> >
> > --- 12年4月18日,周三, Ross <ross.laza...@gmail.com>
> 写道:
> >
> >> 发件人: Ross <ross.laza...@gmail.com>
> >> 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: "Jennifer Jackson" <j...@bx.psu.edu>,
> galaxy-dev@lists.bx.psu.edu
> >> 日期: 2012年4月18日,周三,上午4:59
> >> 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;
> >>
> 
> 
> 
> -- 
> Ross Lazarus MBBS MPH;
> Associate Professor, Harvard Medical School;
> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
> 

___________________________________________________________
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/

Reply via email to