Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found
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:$PATH I used the same way to set other programs, such as bwa and bowtie, and they worked perfectly. Only samtools could not work. I even used the full path of samtools in the wrapper file sam_to_bam.py, and it was not working neither. I am wondering if any one met the same problem, or some one can give me some hints. Thank you very much. Cai
Hi Cai, Please double check that your env.sh file contains the following: PATH="/mnt/galaxyTools/tools/samtools/0.1.12:$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:
-- Jennifer Jackson http://galaxyproject.org
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
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",
drm_job_state.job_wrapper.finish( stdout, stderr ) File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/__init__.py",
dataset.set_meta( overwrite = False ) File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/model/__init__.py",
return self.datatype.set_meta( self, **kwd ) File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/datatypes/binary.py",
On 4/16/12 12:43 PM, zhengqiu cai wrote: line 336, in finish_job line 637, in finish line 875, in set_meta 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:$PATH
I used the same way to set other programs, such as bwa and bowtie, and they worked perfectly. Only samtools could not work. I even used the full path of samtools in the wrapper file sam_to_bam.py, and it was not working neither.
I am wondering if any one met the same problem, or some one can give me some hints.
Thank you very much.
Cai
___________________________________________________________
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org
Cai - if you are using SGE you probably want to pass the Galaxy user's path to the job using the -V switch in the system wide (or Galaxy user's home directory) sge_request file eg I have rlazarus@iaas1-int:~$ 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:$PATH" export PATH
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
Hopefully this helps,
Jen Galaxy team
Hi All,
I was trying to setup the Galaxy tool dependencies, and I met the following problem when running sam-to-bam in samtools: Traceback (most recent call last): File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
On 4/16/12 12:43 PM, zhengqiu cai wrote: line 336, in finish_job
drm_job_state.job_wrapper.finish(
File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/__init__.py",
stdout, stderr ) line 637, in finish
dataset.set_meta( overwrite = False
File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/model/__init__.py",
) line 875, in set_meta
return self.datatype.set_meta(
File "/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/datatypes/binary.py",
self, **kwd ) line 179, in set_meta
raise Exception, "Error Setting BAM
Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found
I already set the path of samtools Below I pasted how I set the path: ubuntu@master:/mnt/galaxyTools/tools/samtools$ 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:$PATH
I used the same way to set other programs, such as bwa and bowtie, and they worked perfectly. Only samtools could not work. I even used the full path of samtools in the wrapper file sam_to_bam.py, and it was not working neither.
I am wondering if any one met the same problem, or some one can give me some hints.
Thank you very much.
Cai
___________________________________________________________
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
Hi Ross, Thank you for your reply. I tried it, and it was still not working. Only samtools has this problem, and the other tools works fine. samtools was compiled from source correctly. If I install samtools using "sudo apt-get install samtools", this problem is gone, but this is not a solution for since it does not work across the cluster. Cai --- 12年4月18日，周三, Ross <ross.lazarus@gmail.com> 写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午4:59 Cai - if you are using SGE you probably want to pass the Galaxy user's path to the job using the -V switch in the system wide (or Galaxy user's home directory) sge_request file
eg I have rlazarus@iaas1-int:~$ 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.
Hi Jen,
Thank you for your quick response. I changed the env.sh file to what you seggested, and
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",
drm_job_state.job_wrapper.finish( stdout, stderr ) File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/__init__.py",
dataset.set_meta( overwrite = False ) File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/model/__init__.py",
return self.datatype.set_meta( self, **kwd ) File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/datatypes/binary.py",
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
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
On Tue, Apr 17, 2012 at 4:26 PM, zhengqiu cai <caizhq2005@yahoo.com.cn> wrote: the problem still existed. line 336, in finish_job line 637, in finish line 875, in set_meta line 179, in set_meta the 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:
-- 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:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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.
Hi Jen,
Thank you for your quick response. I changed the env.sh file to what you seggested, and
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",
drm_job_state.job_wrapper.finish( stdout, stderr ) File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/__init__.py",
dataset.set_meta( overwrite = False ) File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/model/__init__.py",
return self.datatype.set_meta( self, **kwd ) File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/datatypes/binary.py",
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
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:$PATH
I used the same way to set other programs,
such as bwa and bowtie, and they worked perfectly. Only samtools could not work.
I even used the full path of samtools in the wrapper file sam_to_bam.py, and it was not working neither.
I am wondering if any one met the same
On Tue, Apr 17, 2012 at 4:26 PM, zhengqiu cai <caizhq2005@yahoo.com.cn> wrote: the problem still existed. line 336, in finish_job line 637, in finish line 875, in set_meta line 179, in set_meta the problem, or some
one can give me some hints.
Thank you very much.
Cai
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org
___________________________________________________________
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
Hi Ross, Thank you for your reply. It still did not work. I think SGE knows the path of samtools. Here is a test case I added to Galaxy, and it creates the index for fasta file. I pasted the samtools faidx wrapper and xml files below: ubuntu@master:/mnt/galaxyTools/galaxy-dist/tools/samtools$ 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 ${on_string}: fasta" /> </outputs> </tool> It works, which shows that SGE knows the path of samtools. Cai --- 12年4月18日，周三, Ross <ross.lazarus@gmail.com> 写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午5:18 Ah. Then you probably have a library path problem. Here's how we do it FWIW:
Assume your want your shared cluster apps in /data/apps/bin
To share the compiled libraries and binaries together, remember to compile apps like samtools using the --prefix /data/app flag so then you can add the /data/app/lib path to the galaxy user's path so the nodes running jobs inherit those paths because of the -V switch.
I hope this works!
Hi Ross,
Thank you for your reply. I tried it, and it was still not working. Only samtools has this problem, and the other tools works fine.
samtools was compiled from source correctly. If I install samtools using "sudo apt-get install samtools", this
On Tue, Apr 17, 2012 at 5:10 PM, zhengqiu cai <caizhq2005@yahoo.com.cn> wrote: problem is gone, but this is not a solution for since it does not work across the cluster.
Cai
--- 12年4月18日，周三, Ross <ross.lazarus@gmail.com>
写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error Setting
收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午4:59 Cai - if you are using SGE you probably want to pass the Galaxy user's path to the job using the -V switch in the system wide (or Galaxy user's home
sge_request file
eg I have rlazarus@iaas1-int:~$ 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
On Tue, Apr 17, 2012 at 4:26 PM, zhengqiu cai
<caizhq2005@yahoo.com.cn>
Hi Jen,
Thank you for your quick response. I changed the env.sh file to what you seggested, and
wrote: the problem still existed.
I am pasting more details below:
I submitted a job to convert sam to bam, and
was running forever without outputing the result. I
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
documentation:
1. put the path in the env.sh in the tool
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
Then I checked the job log file in the
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
job_working_directory, and it read: 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
BAM Metadata: /bin/sh: samtools: not found directory) path. the job then the Galaxy directory and problem. programs,
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
such as bwa 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:
-- 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:
-- 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;
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 ${on_string}: fasta" /> </outputs> </tool>
It works, which shows that SGE knows the path of samtools.
Cai
--- 12年4月18日，周三, Ross <ross.lazarus@gmail.com> 写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午5:18 Ah. Then you probably have a library path problem. Here's how we do it FWIW:
Assume your want your shared cluster apps in /data/apps/bin
To share the compiled libraries and binaries together, remember to compile apps like samtools using the --prefix /data/app flag so then you can add the /data/app/lib path to the galaxy user's path so the nodes running jobs inherit those paths because of the -V switch.
I hope this works!
Hi Ross,
Thank you for your reply. I tried it, and it was still not working. Only samtools has this problem, and the other tools works fine.
samtools was compiled from source correctly. If I install samtools using "sudo apt-get install samtools", this
On Tue, Apr 17, 2012 at 5:10 PM, zhengqiu cai <caizhq2005@yahoo.com.cn> wrote: problem is gone, but this is not a solution for since it does not work across the cluster.
Cai
--- 12年4月18日，周三, Ross <ross.lazarus@gmail.com>
写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error Setting
收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午4:59 Cai - if you are using SGE you probably want to pass the Galaxy user's path to the job using the -V switch in the system wide (or Galaxy user's home
sge_request file
eg I have rlazarus@iaas1-int:~$ 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
On Tue, Apr 17, 2012 at 4:26 PM, zhengqiu cai
<caizhq2005@yahoo.com.cn>
Hi Jen,
Thank you for your quick response. I changed the env.sh file to what you seggested, and
wrote: the problem still existed.
I am pasting more details below:
I submitted a job to convert sam to bam, and
was running forever without outputing the result. I
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
documentation:
1. put the path in the env.sh in the tool
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
Then I checked the job log file in the
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
job_working_directory, and it read: 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
BAM Metadata: /bin/sh: samtools: not found directory) path. the job then the Galaxy directory and problem. programs,
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
such as bwa 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:
-- 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;
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;
<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 $output1 </command> <inputs> <param name="input1" type="data"
</inputs> <outputs> <data format="fai" name="output1" label="${tool.name} on ${on_string}: fasta" /> </outputs> </tool>
It works, which shows that SGE knows the path of samtools.
Cai
--- 12年4月18日，周三, Ross <ross.lazarus@gmail.com> 写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午5:18 Ah. Then you probably have a library path problem. Here's how we do it FWIW:
Assume your want your shared cluster apps in /data/apps/bin
To share the compiled libraries and binaries together, remember to compile apps like samtools using the --prefix /data/app flag so then you can add the /data/app/lib path to
galaxy user's path so the nodes running jobs inherit those paths because of the -V switch.
I hope this works!
Hi Ross,
Thank you for your reply. I tried it, and it was still not working. Only samtools has this problem, and the other tools works fine.
samtools was compiled from source correctly. If I install samtools using "sudo apt-get install samtools", this
On Tue, Apr 17, 2012 at 5:10 PM, zhengqiu cai <caizhq2005@yahoo.com.cn> wrote: problem is gone, but this is not a solution for since it does not work across the cluster.
Cai
--- 12年4月18日，周三, Ross <ross.lazarus@gmail.com>
写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error
收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午4:59 Cai - if you are using SGE you probably want to pass the Galaxy user's path to the job using the -V switch in the system wide (or Galaxy user's home
Setting BAM Metadata: /bin/sh: samtools: not found directory)
sge_request file
eg I have rlazarus@iaas1-int:~$ cat
/var/lib/gridengine/default/common/sge_request
-cwd -V
Without that switch, the job gets no
With -V, it inherits the job submitter's full path.
Hi Jen,
Thank you for your quick response. I changed the env.sh file to what you seggested, and
I am pasting more details below:
I submitted a job to convert sam to bam, and
On Tue, Apr 17, 2012 at 4:26 PM, zhengqiu cai <caizhq2005@yahoo.com.cn> wrote: the problem still existed. 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
to set the PATH in a couple of methods according
documentation:
1. put the path in the env.sh in the tool
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
I tried the Galaxy directory and problem.
Then I checked the job log file in
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
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
> 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
<jen@bx.psu.edu> the
> following: > > > >
PATH="/mnt/galaxyTools/tools/samtools/0.1.12:$PATH"
> export PATH > > > http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies > > > Hopefully this helps, > > Jen > Galaxy team > > On 4/16/12 12:43 PM, zhengqiu cai wrote: > > Hi All, > > > > I was trying to setup the Galaxy tool dependencies, and > I met the following problem when running sam-to-bam in > samtools: > > Traceback (most recent call last): > > File >
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
> line 336, in finish_job > > drm_job_state.job_wrapper.finish( > stdout, stderr ) > > File >
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/__init__.py",
> line 637, in finish > > dataset.set_meta( overwrite = False > ) > > File >
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/model/__init__.py",
> line 875, in set_meta > > return self.datatype.set_meta( > self, **kwd ) > > File >
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/datatypes/binary.py",
> line 179, in set_meta > > raise Exception, "Error Setting BAM > Metadata: %s" % stderr > > Exception: Error Setting BAM Metadata: /bin/sh: > samtools: not found > > > > > > I already set the path of samtools > > Below I pasted how I set the
> > ubuntu@master:/mnt/galaxyTools/tools/samtools$ 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 > >
> > > > I used the same way to set other
PATH=/mnt/galaxyTools/tools/samtools/0.1.12:$PATH programs,
such as bwa
> and bowtie, and they worked
ubuntu@master:/mnt/galaxyTools/galaxy-dist/tools/samtools$ more samtools_faidx.xml format="fasta" label="fasta file to be indexed" /> the path. the PATH. the directory to path: perfectly.
Only
> 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
samtools could 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:
-- 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;
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 <caizhq2005@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.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:
#!/usr/bin/perl use strict; use warnings;
if (@ARGV < 1) { die "Usage:
ubuntu@master:/mnt/galaxyTools/galaxy-dist/tools/samtools$ more samtools_faidx.pl perl $0 <input fasta file>\n";
} `samtools faidx $ARGV[0]`; `cp ${ARGV[0]}.fai $ARGV[1]`; exit;
<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 $output1 </command> <inputs> <param name="input1" type="data"
</inputs> <outputs> <data format="fai" name="output1" label="${tool.name} on ${on_string}: fasta" /> </outputs> </tool>
It works, which shows that SGE knows the path of samtools.
Cai
--- 12年4月18日，周三, Ross <ross.lazarus@gmail.com> 写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午5:18 Ah. Then you probably have a library path problem. Here's how we do it FWIW:
Assume your want your shared cluster apps in /data/apps/bin
To share the compiled libraries and binaries together, remember to compile apps like samtools using the --prefix /data/app flag so then you can add the /data/app/lib path to
galaxy user's path so the nodes running jobs inherit those paths because of the -V switch.
I hope this works!
Hi Ross,
Thank you for your reply. I tried it, and it was still not working. Only samtools has this problem, and the other tools works fine.
samtools was compiled from source correctly. If I install samtools using "sudo apt-get install samtools", this
On Tue, Apr 17, 2012 at 5:10 PM, zhengqiu cai <caizhq2005@yahoo.com.cn> wrote: problem is gone, but this is not a solution for since it does not work across the cluster.
Cai
--- 12年4月18日，周三, Ross <ross.lazarus@gmail.com>
写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error
收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午4:59 Cai - if you are using SGE you probably want to pass the Galaxy user's path to the job using the -V switch in the system wide (or Galaxy user's home
Setting BAM Metadata: /bin/sh: samtools: not found directory)
sge_request file
eg I have rlazarus@iaas1-int:~$ cat
/var/lib/gridengine/default/common/sge_request
-cwd -V
Without that switch, the job gets no
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
to set the PATH in a couple of methods according
documentation: > 1. put the path in the env.sh in the tool
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
I tried the Galaxy directory and problem.
> > Then I checked the job log file in
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
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:$PATH"
>> export PATH >> >> >> http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies >> >> >> Hopefully this helps, >> >> Jen >> Galaxy team >> >> On 4/16/12 12:43 PM, zhengqiu cai wrote: >> > Hi All, >> > >> > I was trying to setup the Galaxy tool dependencies, and >> I met the following problem when running sam-to-bam in >> samtools: >> > Traceback (most recent call last): >> > File >>
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
>> line 336, in finish_job >> > drm_job_state.job_wrapper.finish( >> stdout, stderr ) >> > File >>
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/__init__.py",
>> line 637, in finish >> > dataset.set_meta( overwrite = False >> ) >> > File >>
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/model/__init__.py",
>> line 875, in set_meta >> > return self.datatype.set_meta( >> self, **kwd ) >> > File >>
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/datatypes/binary.py",
>> line 179, in set_meta >> > raise Exception, "Error Setting BAM >> Metadata: %s" % stderr >> > Exception: Error Setting BAM Metadata: /bin/sh: >> samtools: not found >> > >> > >> > I already set the path of samtools >> > Below I pasted how I set the
>> > ubuntu@master:/mnt/galaxyTools/tools/samtools$ 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 >> >
>> > >> > I used the same way to set other
PATH=/mnt/galaxyTools/tools/samtools/0.1.12:$PATH programs,
such as bwa >> and bowtie, and they worked
ubuntu@master:/mnt/galaxyTools/galaxy-dist/tools/samtools$ more samtools_faidx.xml format="fasta" label="fasta file to be indexed" /> the path. the PATH. the directory to 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;
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;
Hi Cai, Can you check that you have 'set_metadata_externally = True' in your universe_wsgi.ini file? This allows the set_meta process to occur on the nodes as part of the job. Otherwise, you will need to make sure that samtools is installed for the headnode. Thanks for using Galaxy, Dan On Apr 18, 2012, at 11:39 AM, zhengqiu cai 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.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:
#!/usr/bin/perl use strict; use warnings;
if (@ARGV < 1) { die "Usage:
ubuntu@master:/mnt/galaxyTools/galaxy-dist/tools/samtools$ more samtools_faidx.pl perl $0 <input fasta file>\n";
} `samtools faidx $ARGV[0]`; `cp ${ARGV[0]}.fai $ARGV[1]`; exit;
<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 $output1 </command> <inputs> <param name="input1" type="data"
</inputs> <outputs> <data format="fai" name="output1" label="${tool.name} on ${on_string}: fasta" /> </outputs> </tool>
It works, which shows that SGE knows the path of samtools.
Cai
--- 12年4月18日，周三, Ross <ross.lazarus@gmail.com> 写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午5:18 Ah. Then you probably have a library path problem. Here's how we do it FWIW:
Assume your want your shared cluster apps in /data/apps/bin
To share the compiled libraries and binaries together, remember to compile apps like samtools using the --prefix /data/app flag so then you can add the /data/app/lib path to
galaxy user's path so the nodes running jobs inherit those paths because of the -V switch.
I hope this works!
Hi Ross,
Thank you for your reply. I tried it, and it was still not working. Only samtools has this problem, and the other tools works fine.
samtools was compiled from source correctly. If I install samtools using "sudo apt-get install samtools", this
On Tue, Apr 17, 2012 at 5:10 PM, zhengqiu cai <caizhq2005@yahoo.com.cn> wrote: problem is gone, but this is not a solution for since it does not work across the cluster.
Cai
--- 12年4月18日，周三, Ross <ross.lazarus@gmail.com>
写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error
收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午4:59 Cai - if you are using SGE you probably want to pass the Galaxy user's path to the job using the -V switch in the system wide (or Galaxy user's home
Setting BAM Metadata: /bin/sh: samtools: not found directory)
sge_request file
eg I have rlazarus@iaas1-int:~$ cat
/var/lib/gridengine/default/common/sge_request
-cwd -V
Without that switch, the job gets no
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
to set the PATH in a couple of methods according
documentation: > 1. put the path in the env.sh in the tool
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
I tried the Galaxy directory and problem.
> > Then I checked the job log file in
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
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:$PATH"
>> export PATH >> >> >> http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies >> >> >> Hopefully this helps, >> >> Jen >> Galaxy team >> >> On 4/16/12 12:43 PM, zhengqiu cai wrote: >>> Hi All, >>> >>> I was trying to setup the Galaxy tool dependencies, and >> I met the following problem when running sam-to-bam in >> samtools: >>> Traceback (most recent call last): >>> File >>
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
>> line 336, in finish_job >>> drm_job_state.job_wrapper.finish( >> stdout, stderr ) >>> File >>
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/__init__.py",
>> line 637, in finish >>> dataset.set_meta( overwrite = False >> ) >>> File >>
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/model/__init__.py",
>> line 875, in set_meta >>> return self.datatype.set_meta( >> self, **kwd ) >>> File >>
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/datatypes/binary.py",
>> line 179, in set_meta >>> raise Exception, "Error Setting BAM >> Metadata: %s" % stderr >>> Exception: Error Setting BAM Metadata: /bin/sh: >> samtools: not found >>> >>> >>> I already set the path of samtools >>> Below I pasted how I set the
>>> ubuntu@master:/mnt/galaxyTools/tools/samtools$ 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 >>>
>>> >>> I used the same way to set other
PATH=/mnt/galaxyTools/tools/samtools/0.1.12:$PATH programs,
such as bwa >> and bowtie, and they worked
ubuntu@master:/mnt/galaxyTools/galaxy-dist/tools/samtools$ more samtools_faidx.xml format="fasta" label="fasta file to be indexed" /> the path. the PATH. the directory to 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;
___________________________________________________________ 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:
Hi Dan, This is exactly the problem. By default, it was set to False. It works by uncommenting this line and changing it to True. Thank you very much. Cai --- 12年4月18日，周三, Daniel Blankenberg <dan@bx.psu.edu> 写道： 发件人: Daniel Blankenberg <dan@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: "Ross" <ross.lazarus@gmail.com>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,下午11:47 Hi Cai, Can you check that you have 'set_metadata_externally = True' in your universe_wsgi.ini file? This allows the set_meta process to occur on the nodes as part of the job. Otherwise, you will need to make sure that samtools is installed for the headnode. Thanks for using Galaxy, Dan On Apr 18, 2012, at 11:39 AM, zhengqiu cai 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.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 ___________________________________________________________ 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; ___________________________________________________________ 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/
participants (4)
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Daniel Blankenberg -
Jennifer Jackson -
Ross -
zhengqiu cai