Hi Ross, I have a cloudman version of Galaxy working well. What I am doing now is trying to install Galaxy on starcluster, which is a SGE cluster. I should followed the install method for the normal cluster/SGE install, not for the cloud. Thank you for your quick reply. Have a nice day. Cai --- 12年4月18日，周三, Ross <ross.lazarus@gmail.com> 写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,下午11:46 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.
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.lazarus@gmail.com> 写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@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 <caizhq2005@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 $ARGV[1]`; exit;
ubuntu@master:/mnt/galaxyTools/galaxy-dist/tools/samtools$
<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 $output1 </command> <inputs> <param name="input1" type="data"
more samtools_faidx.xml format="fasta" label="fasta file to be indexed" />
</inputs> <outputs> <data format="fai" name="output1" label="${tool.name} on ${on_string}: fasta" /> </outputs> </tool>
It works, which shows that SGE knows the path of samtools.
Cai
--- 12年4月18日，周三, Ross <ross.lazarus@gmail.com> 写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午5:18 Ah. Then you probably have a library path problem. Here's how we do it FWIW:
Assume your want your shared cluster apps in /data/apps/bin
To share the compiled libraries and binaries together, remember to compile apps like samtools using the --prefix /data/app flag so then you can add the /data/app/lib
the
galaxy user's path so the nodes running jobs inherit
because
of the -V switch.
I hope this works!
On Tue, Apr 17, 2012 at 5:10 PM, zhengqiu cai <caizhq2005@yahoo.com.cn> wrote:
Hi Ross,
Thank you for your reply. I tried it, and it was still not working. Only samtools has this problem, and
works fine.
samtools was compiled from source
correctly. If I install samtools using "sudo apt-get install samtools", this problem is gone, but this is not a solution for since it does not work across the cluster.
Cai
--- 12年4月18日，周三, Ross
<ross.lazarus@gmail.com> 写道：
> 发件人: Ross <ross.lazarus@gmail.com> > 主题: Re: [galaxy-dev]
> 收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> > 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu > 日期: 2012年4月18日,周三,上午4:59 > Cai - if you are using SGE you > probably want to pass the Galaxy user's > path to the job using the > -V > switch in the system wide (or Galaxy user's home
Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found directory)
> sge_request file > > eg I have > rlazarus@iaas1-int:~$ cat > /var/lib/gridengine/default/common/sge_request > -cwd > -V > > Without that switch, the job gets no
tools path.
> With -V, it inherits the job submitter's full path. > > On Tue, Apr 17, 2012 at 4:26 PM, zhengqiu cai <caizhq2005@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
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
e.g. the
> job_working_directory, and it read: > > Samtools Version: 0.1.18 (r982:295) > > SAM file converted to BAM > > > > which shows that sge knows
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
of directory to
set the
> tool path) > > > > > > Thanks you very much, > > > > Cai > > --- 12年4月18日，周三, Jennifer Jackson <jen@bx.psu.edu> > 写道： > > > >> 发件人: Jennifer Jackson <jen@bx.psu.edu> > >> 主题: Re: [galaxy-dev] Exception: Error Setting > BAM Metadata: /bin/sh: samtools: not found > >> 收件人: "zhengqiu cai" <caizhq2005@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:$PATH"
> >> export PATH > >> > >> > >> http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies > >> > >> > >> Hopefully this helps, > >> > >> Jen > >> Galaxy team > >> > >> On 4/16/12 12:43 PM, zhengqiu cai wrote: > >> > Hi All, > >> > > >> > I was trying to setup the Galaxy tool > dependencies, and > >> I met the following
running
sam-to-bam
> in > >> samtools: > >> > Traceback (most recent call last): > >> > File > >> >
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
> >> line 336, in finish_job > >> > > drm_job_state.job_wrapper.finish( > >> stdout, stderr ) > >> > File > >> >
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/__init__.py",
> >> line 637, in finish > >> > dataset.set_meta( > overwrite = False > >> ) > >> > File > >> >
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/model/__init__.py",
> >> line 875, in set_meta > >> > return > self.datatype.set_meta( > >> self, **kwd ) > >> > File > >> >
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/datatypes/binary.py",
> >> line 179, in set_meta > >> > raise Exception, "Error > Setting BAM > >> Metadata: %s" % stderr > >> > Exception: Error Setting BAM Metadata: > /bin/sh: > >> samtools: not found > >> > > >> > > >> > I already set the
On Wed, Apr 18, 2012 at 11:39 AM, zhengqiu cai <caizhq2005@yahoo.com.cn> wrote: path to those paths the other directory, the PATH problem when path of
> >> > Below I pasted how I set the
> >> >
ubuntu@master:/mnt/galaxyTools/tools/samtools$
> 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
samtools path: 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;