Re: [galaxy-dev] cluster path question
Ann Black wrote:
> Thanks Nate! I did not know about sge_request - and that helps. I played
> around with using -V and -v in sge_request some and it works similar to
> specifying -V (or -v) in my universe_wsgi.ini file. I am new to galaxy and I
> am working on getting it instantiated locally. Is there an advantage to
> setting my native DRMAA options in my galaxy user's local .sge_request file
> vs. directly in the universe_wsgi.ini configuration file? Would an advantage
> be that I can set more universal drmaa native options that I would like to
> common for all tools there (sge_request for galaxy user) vs. duplicating the
> in each per tool configurations in universe_wsgi file?
Hi Ann,
It probably doesn't matter whether you use .sge_request or the runner
URL in the Galaxy config. The difference may simply be that
.sge_request would be a little less messy.
--nate
>
> Thanks again,
>
> Ann
>
> On Sep 12, 2011, at 12:50 PM, Nate Coraor wrote:
>
> > Ann Black wrote:
> >> I figured out a solution. The sun grid engine will strip back the env of
> >> what gets passed along with the job submission. I added a native drmaa
> >> option, -V, which caused the env vars found on the shell that submits the
> >> job to be passed along. Therefore all the environment setup I did in my
> >> galaxy user's .bash_profile and thus configured in my local shell running
> >> galaxy now gets propagated with my job submissions. This does not allow
> >> changes to .bash_profile to be picked up dynamically, however, since the
> >> .bash_profile is not sourced on each compute node. IE changes made to the
> >> galaxy user's env needs to be re-sourced in the shell that runs galaxy and
> >> dispatches the jobs.
> >>
> >> Thanks - hope this helps others,
> >
> > Hi Ann,
> >
> > For SGE, you can also use ~/.sge_request to set up the environment on
> > the execution host.
> >
> > --nate
> >
> >>
> >> Ann
> >>
> >>
> >> On Sep 12, 2011, at 10:09 AM, Ann Black wrote:
> >>
> >>> Hello everyone -
> >>>
> >>> I am also running into this issue trying to get galaxy integrated with
> >>> our sun grid engine. My galaxy user's .bash_profile does not appear to
> >>> get sourced when the jobs run. I augmented the sample sam_filter.py
> >>> tutorial such that it output path and user info so I could see how the
> >>> jobs were being run:
> >>>
> >>> out = open( sys.argv[2], "w" )
> >>> out2 = open("/data/galaxy-dist/ann.out", "w")
> >>> out2.write(socket.gethostname())
> >>> out2.write("\n")
> >>> out2.write(os.environ['PATH'])
> >>> out2.write("\n")
> >>> drmaa = os.environ.get('DRMAA_LIBRARY_PATH')
> >>> if drmaa is None:
> >>> out2.write("None")
> >>> else:
> >>> out2.write(os.environ.get('DRMAA_LIBRARY_PATH'))
> >>> out2.write("\n")
> >>> out2.write(str(os.geteuid()))
> >>> out2.write("\n")
> >>> out2.write(str(os.getegid()))
> >>> shutil.copytree("/data/galaxy-dist/database/pbs","/data/galaxy-dist/ann")
> >>>
> >>> the job is being dispatched as my galaxy user, however the my augments to
> >>> PATH and additional env vars that I have exported in our galaxy user's
> >>> .bash_profile are not present when the script runs (ie, .bash_profile is
> >>> not sourced). When I use qsub to manually run the galaxy script that
> >>> gets generated under database/pbs, the output to ann.out reflects my PATH
> >>> and exported env vars.
> >>>
> >>> Was there any other solution to this issue besides the drmaa.py script
> >>> augment?
> >>>
> >>> Thanks much for your help,
> >>>
> >>> Ann
> >>
> >>
> >> ___
> >> 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/
>
>
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Re: [galaxy-dev] cluster path question
Thanks Nate! I did not know about sge_request - and that helps. I played
around with using -V and -v in sge_request some and it works similar to
specifying -V (or -v) in my universe_wsgi.ini file. I am new to galaxy and I
am working on getting it instantiated locally. Is there an advantage to
setting my native DRMAA options in my galaxy user's local .sge_request file
vs. directly in the universe_wsgi.ini configuration file? Would an advantage
be that I can set more universal drmaa native options that I would like to
common for all tools there (sge_request for galaxy user) vs. duplicating the in
each per tool configurations in universe_wsgi file?
Thanks again,
Ann
On Sep 12, 2011, at 12:50 PM, Nate Coraor wrote:
> Ann Black wrote:
>> I figured out a solution. The sun grid engine will strip back the env of
>> what gets passed along with the job submission. I added a native drmaa
>> option, -V, which caused the env vars found on the shell that submits the
>> job to be passed along. Therefore all the environment setup I did in my
>> galaxy user's .bash_profile and thus configured in my local shell running
>> galaxy now gets propagated with my job submissions. This does not allow
>> changes to .bash_profile to be picked up dynamically, however, since the
>> .bash_profile is not sourced on each compute node. IE changes made to the
>> galaxy user's env needs to be re-sourced in the shell that runs galaxy and
>> dispatches the jobs.
>>
>> Thanks - hope this helps others,
>
> Hi Ann,
>
> For SGE, you can also use ~/.sge_request to set up the environment on
> the execution host.
>
> --nate
>
>>
>> Ann
>>
>>
>> On Sep 12, 2011, at 10:09 AM, Ann Black wrote:
>>
>>> Hello everyone -
>>>
>>> I am also running into this issue trying to get galaxy integrated with our
>>> sun grid engine. My galaxy user's .bash_profile does not appear to get
>>> sourced when the jobs run. I augmented the sample sam_filter.py tutorial
>>> such that it output path and user info so I could see how the jobs were
>>> being run:
>>>
>>> out = open( sys.argv[2], "w" )
>>> out2 = open("/data/galaxy-dist/ann.out", "w")
>>> out2.write(socket.gethostname())
>>> out2.write("\n")
>>> out2.write(os.environ['PATH'])
>>> out2.write("\n")
>>> drmaa = os.environ.get('DRMAA_LIBRARY_PATH')
>>> if drmaa is None:
>>> out2.write("None")
>>> else:
>>> out2.write(os.environ.get('DRMAA_LIBRARY_PATH'))
>>> out2.write("\n")
>>> out2.write(str(os.geteuid()))
>>> out2.write("\n")
>>> out2.write(str(os.getegid()))
>>> shutil.copytree("/data/galaxy-dist/database/pbs","/data/galaxy-dist/ann")
>>>
>>> the job is being dispatched as my galaxy user, however the my augments to
>>> PATH and additional env vars that I have exported in our galaxy user's
>>> .bash_profile are not present when the script runs (ie, .bash_profile is
>>> not sourced). When I use qsub to manually run the galaxy script that gets
>>> generated under database/pbs, the output to ann.out reflects my PATH and
>>> exported env vars.
>>>
>>> Was there any other solution to this issue besides the drmaa.py script
>>> augment?
>>>
>>> Thanks much for your help,
>>>
>>> Ann
>>
>>
>> ___
>> 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/
___
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Re: [galaxy-dev] cluster path question
Ann Black wrote:
> I figured out a solution. The sun grid engine will strip back the env of
> what gets passed along with the job submission. I added a native drmaa
> option, -V, which caused the env vars found on the shell that submits the job
> to be passed along. Therefore all the environment setup I did in my galaxy
> user's .bash_profile and thus configured in my local shell running galaxy now
> gets propagated with my job submissions. This does not allow changes to
> .bash_profile to be picked up dynamically, however, since the .bash_profile
> is not sourced on each compute node. IE changes made to the galaxy user's
> env needs to be re-sourced in the shell that runs galaxy and dispatches the
> jobs.
>
> Thanks - hope this helps others,
Hi Ann,
For SGE, you can also use ~/.sge_request to set up the environment on
the execution host.
--nate
>
> Ann
>
>
> On Sep 12, 2011, at 10:09 AM, Ann Black wrote:
>
> > Hello everyone -
> >
> > I am also running into this issue trying to get galaxy integrated with our
> > sun grid engine. My galaxy user's .bash_profile does not appear to get
> > sourced when the jobs run. I augmented the sample sam_filter.py tutorial
> > such that it output path and user info so I could see how the jobs were
> > being run:
> >
> > out = open( sys.argv[2], "w" )
> > out2 = open("/data/galaxy-dist/ann.out", "w")
> > out2.write(socket.gethostname())
> > out2.write("\n")
> > out2.write(os.environ['PATH'])
> > out2.write("\n")
> > drmaa = os.environ.get('DRMAA_LIBRARY_PATH')
> > if drmaa is None:
> > out2.write("None")
> > else:
> > out2.write(os.environ.get('DRMAA_LIBRARY_PATH'))
> > out2.write("\n")
> > out2.write(str(os.geteuid()))
> > out2.write("\n")
> > out2.write(str(os.getegid()))
> > shutil.copytree("/data/galaxy-dist/database/pbs","/data/galaxy-dist/ann")
> >
> > the job is being dispatched as my galaxy user, however the my augments to
> > PATH and additional env vars that I have exported in our galaxy user's
> > .bash_profile are not present when the script runs (ie, .bash_profile is
> > not sourced). When I use qsub to manually run the galaxy script that gets
> > generated under database/pbs, the output to ann.out reflects my PATH and
> > exported env vars.
> >
> > Was there any other solution to this issue besides the drmaa.py script
> > augment?
> >
> > Thanks much for your help,
> >
> > Ann
>
>
> ___
> 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/
___
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] cluster path question
I figured out a solution. The sun grid engine will strip back the env of what
gets passed along with the job submission. I added a native drmaa option, -V,
which caused the env vars found on the shell that submits the job to be passed
along. Therefore all the environment setup I did in my galaxy user's
.bash_profile and thus configured in my local shell running galaxy now gets
propagated with my job submissions. This does not allow changes to
.bash_profile to be picked up dynamically, however, since the .bash_profile is
not sourced on each compute node. IE changes made to the galaxy user's env
needs to be re-sourced in the shell that runs galaxy and dispatches the jobs.
Thanks - hope this helps others,
Ann
On Sep 12, 2011, at 10:09 AM, Ann Black wrote:
> Hello everyone -
>
> I am also running into this issue trying to get galaxy integrated with our
> sun grid engine. My galaxy user's .bash_profile does not appear to get
> sourced when the jobs run. I augmented the sample sam_filter.py tutorial such
> that it output path and user info so I could see how the jobs were being run:
>
> out = open( sys.argv[2], "w" )
> out2 = open("/data/galaxy-dist/ann.out", "w")
> out2.write(socket.gethostname())
> out2.write("\n")
> out2.write(os.environ['PATH'])
> out2.write("\n")
> drmaa = os.environ.get('DRMAA_LIBRARY_PATH')
> if drmaa is None:
> out2.write("None")
> else:
> out2.write(os.environ.get('DRMAA_LIBRARY_PATH'))
> out2.write("\n")
> out2.write(str(os.geteuid()))
> out2.write("\n")
> out2.write(str(os.getegid()))
> shutil.copytree("/data/galaxy-dist/database/pbs","/data/galaxy-dist/ann")
>
> the job is being dispatched as my galaxy user, however the my augments to
> PATH and additional env vars that I have exported in our galaxy user's
> .bash_profile are not present when the script runs (ie, .bash_profile is not
> sourced). When I use qsub to manually run the galaxy script that gets
> generated under database/pbs, the output to ann.out reflects my PATH and
> exported env vars.
>
> Was there any other solution to this issue besides the drmaa.py script
> augment?
>
> Thanks much for your help,
>
> Ann
___
Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] cluster path question
Hello everyone -
I am also running into this issue trying to get galaxy integrated with our sun
grid engine. My galaxy user's .bash_profile does not appear to get sourced
when the jobs run. I augmented the sample sam_filter.py tutorial such that it
output path and user info so I could see how the jobs were being run:
out = open( sys.argv[2], "w" )
out2 = open("/data/galaxy-dist/ann.out", "w")
out2.write(socket.gethostname())
out2.write("\n")
out2.write(os.environ['PATH'])
out2.write("\n")
drmaa = os.environ.get('DRMAA_LIBRARY_PATH')
if drmaa is None:
out2.write("None")
else:
out2.write(os.environ.get('DRMAA_LIBRARY_PATH'))
out2.write("\n")
out2.write(str(os.geteuid()))
out2.write("\n")
out2.write(str(os.getegid()))
shutil.copytree("/data/galaxy-dist/database/pbs","/data/galaxy-dist/ann")
the job is being dispatched as my galaxy user, however the my augments to PATH
and additional env vars that I have exported in our galaxy user's .bash_profile
are not present when the script runs (ie, .bash_profile is not sourced). When
I use qsub to manually run the galaxy script that gets generated under
database/pbs, the output to ann.out reflects my PATH and exported env vars.
Was there any other solution to this issue besides the drmaa.py script augment?
Thanks much for your help,
Ann
___
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in your mail client. To manage your subscriptions to this
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Re: [galaxy-dev] cluster path question
On 2/18/11 2:37 PM, Glen Beane wrote: On Feb 18, 2011, at 2:12 PM, Ryan Golhar wrote: It turns out the user's environment is not set up for batch jobs, only the system environment. I too added ". ~/.bashrc" to lib/galaxy/jobs/runners/drmaa.py. I'm afraid this is a kludgy fix that will break if/when the drmaa.py file gets updated. It'll work for now, but there has got to be a better way. I use TORQUE, but I don't use the drmaa runner. In my case I have no problems with setting the PATH in the .bashrc for the galaxy user on my cluster. Is there a particular reason why you want to use the drmaa runner instead of the PBS runner if your cluster uses TORQUE? I couldn't get the pbs_runner to work...so I went with drmaa. On 2/18/11 1:30 PM, Zhibin Lu wrote: Hi, I had same problem since we do not install software in the system directory. I had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py manually. I do not know if anyone has better solution. Zhibin Lu Bioinformatics Support Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 www.oicr.on.ca Date: Fri, 18 Feb 2011 13:17:26 -0500 From: n...@bx.psu.edu To: golha...@umdnj.edu CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cluster path question Ryan Golhar wrote: Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? Hi Ryan, Whatever user is running the jobs will need to modify the $PATH in its shell startup files. If you're using bash, this would probably be ~/.bash_profile It already is in .bashrc (which is called by .bash_profile) for the galaxy user. I can submit the script from the shell and it runs okay so something is up with either how the galaxy app is submitting the job or the environment being used by the galaxy job. When you say submit via the shell, do you mean with qsub, or by logging in to a node and running the wrapper script? I haven't tested Torque with the drmaa runner so perhaps it's submitting in a way which starts the shell in non-interactive, non-login mode. Let me know if you can determine for certain that no shell startup files are being read, and I'll try to replicate this in my environment. I'd like to modify the job script to print out some debugging information to determine what environment variables are set when the job gets executed. Actually, this would be a useful "tool" within Galaxy to test the cluster. That's probably the simplest method, to just create a tool that outputs (either to stdout or the output file) what you'd like to see. begin:vcard fn:Ryan Golhar, Ph.D. n:Golhar;Ryan org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA email;internet:golha...@umdnj.edu title:NGS Bioinformatics Specialist tel;work:(732) 235-6613 tel;fax:(732) 235-6267 tel;cell:(732) 236-1176 x-mozilla-html:FALSE url:http://www.cinj.org version:2.1 end:vcard ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153 ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delet
Re: [galaxy-dev] cluster path question
On Feb 18, 2011, at 2:12 PM, Ryan Golhar wrote: > It turns out the user's environment is not set up for batch jobs, only > the system environment. I too added ". ~/.bashrc" to > lib/galaxy/jobs/runners/drmaa.py. > > I'm afraid this is a kludgy fix that will break if/when the drmaa.py > file gets updated. It'll work for now, but there has got to be a better > way. > I use TORQUE, but I don't use the drmaa runner. In my case I have no problems with setting the PATH in the .bashrc for the galaxy user on my cluster. Is there a particular reason why you want to use the drmaa runner instead of the PBS runner if your cluster uses TORQUE? > > On 2/18/11 1:30 PM, Zhibin Lu wrote: >> Hi, >> >> I had same problem since we do not install software in the system >> directory. I had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py >> manually. I do not know if anyone has better solution. >> >> Zhibin Lu >> Bioinformatics Support >> >> Ontario Institute for Cancer Research >> MaRS Centre, South Tower >> 101 College Street, Suite 800 >> Toronto, Ontario, Canada M5G 0A3 >> >> www.oicr.on.ca >> >>> Date: Fri, 18 Feb 2011 13:17:26 -0500 >>> From: n...@bx.psu.edu >>> To: golha...@umdnj.edu >>> CC: galaxy-dev@lists.bx.psu.edu >>> Subject: Re: [galaxy-dev] cluster path question >>> >>> Ryan Golhar wrote: >>>> >>>>> Ryan Golhar wrote: >>>>>> I'm setting up Galaxy to run on my cluster using drmaa. I can see >>>>>> jobs getting submitted to Torque however the jobs keep failing, >>>>>> because the tools are in the default system path. >>>>>> >>>>>> How do I tell galaxy to append a directory to the path used by jobs? >>>>> >>>>> Hi Ryan, >>>>> >>>>> Whatever user is running the jobs will need to modify the $PATH in its >>>>> shell startup files. If you're using bash, this would probably be >>>>> ~/.bash_profile >>>> >>>> It already is in .bashrc (which is called by .bash_profile) for the >>>> galaxy user. I can submit the script from the shell and it runs >>>> okay so something is up with either how the galaxy app is submitting >>>> the job or the environment being used by the galaxy job. >>> >>> When you say submit via the shell, do you mean with qsub, or by logging >>> in to a node and running the wrapper script? >>> >>> I haven't tested Torque with the drmaa runner so perhaps it's submitting >>> in a way which starts the shell in non-interactive, non-login mode. Let >>> me know if you can determine for certain that no shell startup files are >>> being read, and I'll try to replicate this in my environment. >>> >>>> I'd like to modify the job script to print out some debugging >>>> information to determine what environment variables are set when the >>>> job gets executed. Actually, this would be a useful "tool" within >>>> Galaxy to test the cluster. >>> >>> That's probably the simplest method, to just create a tool that outputs >>> (either to stdout or the output file) what you'd like to see. >>> >>>> >>> >>>> begin:vcard >>>> fn:Ryan Golhar, Ph.D. >>>> n:Golhar;Ryan >>>> org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics >>>> adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA >>>> email;internet:golha...@umdnj.edu >>>> title:NGS Bioinformatics Specialist >>>> tel;work:(732) 235-6613 >>>> tel;fax:(732) 235-6267 >>>> tel;cell:(732) 236-1176 >>>> x-mozilla-html:FALSE >>>> url:http://www.cinj.org >>>> version:2.1 >>>> end:vcard >>>> >>> >>>> ___ >>>> To manage your subscriptions to this and other Galaxy lists, please >> use the interface at: >>>> >>>> http://lists.bx.psu.edu/ >>> >>> ___ >>> To manage your subscriptions to this and other Galaxy lists, please >> use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> >> >> ___ >> To manage your subscriptions to this and other Galaxy lists, please use the >> interface at: >> >> http://lists.bx.psu.edu/ > > -- > CONFIDENTIALITY NOTICE: This email communication may contain private, > confidential, or legally privileged information intended for the sole > use of the designated and/or duly authorized recipient(s). If you are > not the intended recipient or have received this email in error, please > notify the sender immediately by email and permanently delete all copies > of this email including all attachments without reading them. If you are > the intended recipient, secure the contents in a manner that conforms to > all applicable state and/or federal requirements related to privacy and > confidentiality of such information. > -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153 ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] cluster path question
Ryan Golhar wrote: > It turns out the user's environment is not set up for batch jobs, > only the system environment. I too added ". ~/.bashrc" to > lib/galaxy/jobs/runners/drmaa.py. > > I'm afraid this is a kludgy fix that will break if/when the drmaa.py > file gets updated. It'll work for now, but there has got to be a > better way. I'll work on this and release a fix (or instructions for environment configuration) ASAP. > > > > On 2/18/11 1:30 PM, Zhibin Lu wrote: > >Hi, > > > >I had same problem since we do not install software in the system > >directory. I had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py > >manually. I do not know if anyone has better solution. > > > >Zhibin Lu > >Bioinformatics Support > > > >Ontario Institute for Cancer Research > >MaRS Centre, South Tower > >101 College Street, Suite 800 > >Toronto, Ontario, Canada M5G 0A3 > > > >www.oicr.on.ca > > > > > Date: Fri, 18 Feb 2011 13:17:26 -0500 > > > From: n...@bx.psu.edu > > > To: golha...@umdnj.edu > > > CC: galaxy-dev@lists.bx.psu.edu > > > Subject: Re: [galaxy-dev] cluster path question > > > > > > Ryan Golhar wrote: > > > > > > > > >Ryan Golhar wrote: > > > > >>I'm setting up Galaxy to run on my cluster using drmaa. I can see > > > > >>jobs getting submitted to Torque however the jobs keep failing, > > > > >>because the tools are in the default system path. > > > > >> > > > > >>How do I tell galaxy to append a directory to the path used by jobs? > > > > > > > > > >Hi Ryan, > > > > > > > > > >Whatever user is running the jobs will need to modify the $PATH in its > > > > >shell startup files. If you're using bash, this would probably be > > > > >~/.bash_profile > > > > > > > > It already is in .bashrc (which is called by .bash_profile) for the > > > > galaxy user. I can submit the script from the shell and it runs > > > > okay so something is up with either how the galaxy app is submitting > > > > the job or the environment being used by the galaxy job. > > > > > > When you say submit via the shell, do you mean with qsub, or by logging > > > in to a node and running the wrapper script? > > > > > > I haven't tested Torque with the drmaa runner so perhaps it's submitting > > > in a way which starts the shell in non-interactive, non-login mode. Let > > > me know if you can determine for certain that no shell startup files are > > > being read, and I'll try to replicate this in my environment. > > > > > > > I'd like to modify the job script to print out some debugging > > > > information to determine what environment variables are set when the > > > > job gets executed. Actually, this would be a useful "tool" within > > > > Galaxy to test the cluster. > > > > > > That's probably the simplest method, to just create a tool that outputs > > > (either to stdout or the output file) what you'd like to see. > > > > > > > > > > > > > > begin:vcard > > > > fn:Ryan Golhar, Ph.D. > > > > n:Golhar;Ryan > > > > org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics > > > > adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA > > > > email;internet:golha...@umdnj.edu > > > > title:NGS Bioinformatics Specialist > > > > tel;work:(732) 235-6613 > > > > tel;fax:(732) 235-6267 > > > > tel;cell:(732) 236-1176 > > > > x-mozilla-html:FALSE > > > > url:http://www.cinj.org > > > > version:2.1 > > > > end:vcard > > > > > > > > > > > ___ > > > > To manage your subscriptions to this and other Galaxy lists, please > >use the interface at: > > > > > > > > http://lists.bx.psu.edu/ > > > > > > ___ > > > To manage your subscriptions to this and other Galaxy lists, please > >use the interface at: > > > > > > http://lists.bx.psu.edu/ > > > > > > > >___ > >To manage your subscriptions to this and other Galaxy lists, please use the > >interface at: > > > &g
Re: [galaxy-dev] cluster path question
It turns out the user's environment is not set up for batch jobs, only the system environment. I too added ". ~/.bashrc" to lib/galaxy/jobs/runners/drmaa.py. I'm afraid this is a kludgy fix that will break if/when the drmaa.py file gets updated. It'll work for now, but there has got to be a better way. On 2/18/11 1:30 PM, Zhibin Lu wrote: Hi, I had same problem since we do not install software in the system directory. I had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py manually. I do not know if anyone has better solution. Zhibin Lu Bioinformatics Support Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 www.oicr.on.ca > Date: Fri, 18 Feb 2011 13:17:26 -0500 > From: n...@bx.psu.edu > To: golha...@umdnj.edu > CC: galaxy-dev@lists.bx.psu.edu > Subject: Re: [galaxy-dev] cluster path question > > Ryan Golhar wrote: > > > > >Ryan Golhar wrote: > > >>I'm setting up Galaxy to run on my cluster using drmaa. I can see > > >>jobs getting submitted to Torque however the jobs keep failing, > > >>because the tools are in the default system path. > > >> > > >>How do I tell galaxy to append a directory to the path used by jobs? > > > > > >Hi Ryan, > > > > > >Whatever user is running the jobs will need to modify the $PATH in its > > >shell startup files. If you're using bash, this would probably be > > >~/.bash_profile > > > > It already is in .bashrc (which is called by .bash_profile) for the > > galaxy user. I can submit the script from the shell and it runs > > okay so something is up with either how the galaxy app is submitting > > the job or the environment being used by the galaxy job. > > When you say submit via the shell, do you mean with qsub, or by logging > in to a node and running the wrapper script? > > I haven't tested Torque with the drmaa runner so perhaps it's submitting > in a way which starts the shell in non-interactive, non-login mode. Let > me know if you can determine for certain that no shell startup files are > being read, and I'll try to replicate this in my environment. > > > I'd like to modify the job script to print out some debugging > > information to determine what environment variables are set when the > > job gets executed. Actually, this would be a useful "tool" within > > Galaxy to test the cluster. > > That's probably the simplest method, to just create a tool that outputs > (either to stdout or the output file) what you'd like to see. > > > > > > begin:vcard > > fn:Ryan Golhar, Ph.D. > > n:Golhar;Ryan > > org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics > > adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA > > email;internet:golha...@umdnj.edu > > title:NGS Bioinformatics Specialist > > tel;work:(732) 235-6613 > > tel;fax:(732) 235-6267 > > tel;cell:(732) 236-1176 > > x-mozilla-html:FALSE > > url:http://www.cinj.org > > version:2.1 > > end:vcard > > > > > ___ > > To manage your subscriptions to this and other Galaxy lists, please use the interface at: > > > > http://lists.bx.psu.edu/ > > ___ > To manage your subscriptions to this and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. <>___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] cluster path question
Hi, I had same problem since we do not install software in the system directory. I had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py manually. I do not know if anyone has better solution. Zhibin Lu Bioinformatics Support Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 www.oicr.on.ca > Date: Fri, 18 Feb 2011 13:17:26 -0500 > From: n...@bx.psu.edu > To: golha...@umdnj.edu > CC: galaxy-dev@lists.bx.psu.edu > Subject: Re: [galaxy-dev] cluster path question > > Ryan Golhar wrote: > > > > >Ryan Golhar wrote: > > >>I'm setting up Galaxy to run on my cluster using drmaa. I can see > > >>jobs getting submitted to Torque however the jobs keep failing, > > >>because the tools are in the default system path. > > >> > > >>How do I tell galaxy to append a directory to the path used by jobs? > > > > > >Hi Ryan, > > > > > >Whatever user is running the jobs will need to modify the $PATH in its > > >shell startup files. If you're using bash, this would probably be > > >~/.bash_profile > > > > It already is in .bashrc (which is called by .bash_profile) for the > > galaxy user. I can submit the script from the shell and it runs > > okay so something is up with either how the galaxy app is submitting > > the job or the environment being used by the galaxy job. > > When you say submit via the shell, do you mean with qsub, or by logging > in to a node and running the wrapper script? > > I haven't tested Torque with the drmaa runner so perhaps it's submitting > in a way which starts the shell in non-interactive, non-login mode. Let > me know if you can determine for certain that no shell startup files are > being read, and I'll try to replicate this in my environment. > > > I'd like to modify the job script to print out some debugging > > information to determine what environment variables are set when the > > job gets executed. Actually, this would be a useful "tool" within > > Galaxy to test the cluster. > > That's probably the simplest method, to just create a tool that outputs > (either to stdout or the output file) what you'd like to see. > > > > > > begin:vcard > > fn:Ryan Golhar, Ph.D. > > n:Golhar;Ryan > > org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics > > adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA > > email;internet:golha...@umdnj.edu > > title:NGS Bioinformatics Specialist > > tel;work:(732) 235-6613 > > tel;fax:(732) 235-6267 > > tel;cell:(732) 236-1176 > > x-mozilla-html:FALSE > > url:http://www.cinj.org > > version:2.1 > > end:vcard > > > > > ___ > > To manage your subscriptions to this and other Galaxy lists, please use the > > interface at: > > > > http://lists.bx.psu.edu/ > > ___ > To manage your subscriptions to this and other Galaxy lists, please use the > interface at: > > http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] cluster path question
Ryan Golhar wrote: > > >Ryan Golhar wrote: > >>I'm setting up Galaxy to run on my cluster using drmaa. I can see > >>jobs getting submitted to Torque however the jobs keep failing, > >>because the tools are in the default system path. > >> > >>How do I tell galaxy to append a directory to the path used by jobs? > > > >Hi Ryan, > > > >Whatever user is running the jobs will need to modify the $PATH in its > >shell startup files. If you're using bash, this would probably be > >~/.bash_profile > > It already is in .bashrc (which is called by .bash_profile) for the > galaxy user. I can submit the script from the shell and it runs > okay so something is up with either how the galaxy app is submitting > the job or the environment being used by the galaxy job. When you say submit via the shell, do you mean with qsub, or by logging in to a node and running the wrapper script? I haven't tested Torque with the drmaa runner so perhaps it's submitting in a way which starts the shell in non-interactive, non-login mode. Let me know if you can determine for certain that no shell startup files are being read, and I'll try to replicate this in my environment. > I'd like to modify the job script to print out some debugging > information to determine what environment variables are set when the > job gets executed. Actually, this would be a useful "tool" within > Galaxy to test the cluster. That's probably the simplest method, to just create a tool that outputs (either to stdout or the output file) what you'd like to see. > > begin:vcard > fn:Ryan Golhar, Ph.D. > n:Golhar;Ryan > org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics > adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA > email;internet:golha...@umdnj.edu > title:NGS Bioinformatics Specialist > tel;work:(732) 235-6613 > tel;fax:(732) 235-6267 > tel;cell:(732) 236-1176 > x-mozilla-html:FALSE > url:http://www.cinj.org > version:2.1 > end:vcard > > ___ > To manage your subscriptions to this and other Galaxy lists, please use the > interface at: > > http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] cluster path question
Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? Hi Ryan, Whatever user is running the jobs will need to modify the $PATH in its shell startup files. If you're using bash, this would probably be ~/.bash_profile It already is in .bashrc (which is called by .bash_profile) for the galaxy user. I can submit the script from the shell and it runs okay so something is up with either how the galaxy app is submitting the job or the environment being used by the galaxy job. I'd like to modify the job script to print out some debugging information to determine what environment variables are set when the job gets executed. Actually, this would be a useful "tool" within Galaxy to test the cluster. <>___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] cluster path question
Ryan Golhar wrote: > I'm setting up Galaxy to run on my cluster using drmaa. I can see > jobs getting submitted to Torque however the jobs keep failing, > because the tools are in the default system path. > > How do I tell galaxy to append a directory to the path used by jobs? Hi Ryan, Whatever user is running the jobs will need to modify the $PATH in its shell startup files. If you're using bash, this would probably be ~/.bash_profile --nate > > -- > CONFIDENTIALITY NOTICE: This email communication may contain > private, confidential, or legally privileged information intended > for the sole use of the designated and/or duly authorized > recipient(s). If you are not the intended recipient or have received > this email in error, please notify the sender immediately by email > and permanently delete all copies of this email including all > attachments without reading them. If you are the intended recipient, > secure the contents in a manner that conforms to all applicable > state and/or federal requirements related to privacy and > confidentiality of such information. > begin:vcard > fn:Ryan Golhar, Ph.D. > n:Golhar;Ryan > org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics > adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA > email;internet:golha...@umdnj.edu > title:NGS Bioinformatics Specialist > tel;work:(732) 235-6613 > tel;fax:(732) 235-6267 > tel;cell:(732) 236-1176 > x-mozilla-html:FALSE > url:http://www.cinj.org > version:2.1 > end:vcard > > ___ > To manage your subscriptions to this and other Galaxy lists, please use the > interface at: > > http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] cluster path question
I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. <>___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
