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;
>
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