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 $ARGV[1]`;
exit;
ubuntu@master:/mnt/galaxyTools/galaxy-dist/tools/samtools$
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 ${on_string}: fasta" />
</outputs>
</tool>
It works, which shows that SGE knows the path of
samtools.
Cai
--- 12年4月18日，周三, Ross <ross.lazarus@gmail.com>
写道：
发件人: Ross <ross.lazarus@gmail.com>
主题: Re: [galaxy-dev] Exception: Error Setting
BAM Metadata: /bin/sh: samtools: not found
收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn>
抄送: "Jennifer Jackson" <jen@bx.psu.edu>,
galaxy-dev@lists.bx.psu.edu
日期: 2012年4月18日,周三,上午5:18
Ah. Then you probably have a library
path problem.
Here's how we do it FWIW:
Assume your want your shared cluster apps in
/data/apps/bin
To share the compiled libraries and binaries
together,
remember to
compile apps like samtools using the
--prefix /data/app
flag so then you can add the /data/app/lib path to
the
galaxy user's
path so the nodes running jobs inherit those paths
because
of the -V
switch.
I hope this works!
On Tue, Apr 17, 2012 at 5:10 PM, zhengqiu cai
<caizhq2005@yahoo.com.cn>
wrote:
Hi Ross,
Thank you for your reply.
I tried it, and it was still not working.
Only samtools has this problem, and the other
tools
works fine.
samtools was compiled from source correctly.
If I
install samtools using "sudo apt-get install
samtools", this
problem is gone, but this is not a solution for
since it
does not work across the cluster.
Cai
--- 12年4月18日，周三, Ross <ross.lazarus@gmail.com>
写道：
发件人: Ross <ross.lazarus@gmail.com>
主题: Re: [galaxy-dev] Exception: Error
Setting
BAM Metadata: /bin/sh: samtools: not found
收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn>
抄送: "Jennifer Jackson" <jen@bx.psu.edu>,
galaxy-dev@lists.bx.psu.edu
日期:
2012年4月18日,周三,上午4:59
Cai - if you are using SGE you
probably want to pass the Galaxy user's
path to the job using the
-V
switch in the system wide (or Galaxy
user's home
directory)
sge_request file
eg I have
rlazarus@iaas1-int:~$ 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
<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 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
<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:$PATH"
export PATH
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
Hopefully this helps,
Jen
Galaxy team
On 4/16/12 12:43 PM, zhengqiu cai
wrote:
Hi All,
I was trying to setup the
Galaxy
tool
dependencies, and
I met the following problem when
running
sam-to-bam
in
samtools:
Traceback (most recent call
last):
File
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
line 336, in finish_job
drm_job_state.job_wrapper.finish(
stdout, stderr )
File
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/__init__.py",
line 637, in finish
dataset.set_meta(
overwrite = False
)
File
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/model/__init__.py",
line 875, in set_meta
return
self.datatype.set_meta(
self, **kwd )
File
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/datatypes/binary.py",
line 179, in set_meta
raise
Exception,
"Error
Setting BAM
Metadata: %s" % stderr
Exception: Error Setting
BAM
Metadata:
/bin/sh:
samtools: not found
I already set the path of
samtools
Below I pasted how I set the
path:
ubuntu@master:/mnt/galaxyTools/tools/samtools$
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
___________________________________________________________
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--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
Please keep all replies on the list
by using
"reply
all"
in your mail client. To manage
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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;
___________________________________________________________
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/