Hi, Cai.
Apologies but I had not noticed any reference to the cloud
distribution before - that changes everything - I was talking about a
normal cluster/SGE install - you should definitely not need to do
anything at all to the AMI - maybe someone with cloudman experience
can be more helpful than I can.

On Wed, Apr 18, 2012 at 11:39 AM, zhengqiu cai <caizhq2...@yahoo.com.cn> wrote:
> Hi Ross,
>
> I did not compile samtools using the --prefix. The samtools I used comes with 
> Galaxy AMI image, and I copied it to the same path on my EC2. How to compile 
> samtools using --prefix? I just typed 'make', and there is not a 
> configuration file. In the cloudman version of Galaxy (it is working well for 
> me), only two executables (samtools and maq2sam-long) in the directory 
> /mnt/galaxyTools/tools/samtools/0.1.12. I copies the same files to my EC2. Is 
> the only compiled executable 'samtools' fully functional for the cluster(it 
> is on the local machine)? or should I set some other libraries?
>
> Thank you,
>
> 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,下午11:07
>> Hi, Cai - sorry to hear it's still
>> not working right.
>>
>> You've compiled/installed samtools using the --prefix
>> configure option
>> and tested that all the samtools based Galaxy wrappers work
>> if you use
>> the local job runner? That means that both the appropriate
>> lib and bin
>> directories are on the Galaxy user's path ready to be
>> inherited by SGE
>> with the -V SGE option.
>>
>> If the local job runner works, that seems to isolate the
>> problem to
>> SGE configuration and operation - the steps I've suggested
>> seem to
>> work for us so I've run out of ideas on why it's not working
>> at your
>> shop and hope somebody with more experience can help out.
>>
>>
>> On Wed, Apr 18, 2012 at 10:50 AM, zhengqiu cai <caizhq2...@yahoo.com.cn>
>> wrote:
>> > 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;
>> >>
>>
>>
>>
>> --
>> 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;

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