Re: [galaxy-dev] Galaxy Error Message
Thank you for your patience and help, I removed the periods and am running into this error: /bin/sh: /Users/bbelfio1/galaxy-dist/database/files/000/dataset_25.dat: Permission denied Does it have to do with the fact Im using SQLite and not Postgres? On Tue, Apr 29, 2014 at 1:13 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Bradley, For your inputs, don’t use periods (‘.’) within the param names. Thanks for using Galaxy, Dan On Apr 29, 2014, at 12:32 PM, Bradley Belfiore bradbelf2...@gmail.com wrote: The XML file is: tool id=pathview name=pathview version=1.0 description Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs./description command interpreter=Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $ pathway.id $species $out.suffix $output /command inputs param name=gene.data type=data format=data label=enter input file/ param name=pathway.id type=text format=text label=Pathway ID/ param name=species type=text format=text label=Species/ param name=out.suffix type=text format=text label=Output Suffix / /inputs outputs data format=pdf name=output/ /outputs /tool With basic Rscript : args - commandArgs(TRUE) ## inputs gene.data - args[1] pathway.id - args[2] species -args[3] out.suffix -args[4] output -args[5] suppressMessages(library(pathview)) suppressMessages(library(KEGGgraph)) suppressMessages(library(Rgraphviz)) pv.out - pathview(gene.data=gene.data , pathway.id= pathway.id, species=species, out.suffix=output, kegg.native=T) On Tue, Apr 29, 2014 at 12:26 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Brad To me, this looks like an error in tool definition file (ie the xml file). Something like using $gene in the command tag without defining it in a param tag. But it is difficult to guess without seeing to full xml file. Regards Hans-Rudolf On 04/29/2014 06:13 PM, Bradley Belfiore wrote: Upon going back over my script I got it working on the command line as suggested, and when attempting to execute in my instance of galaxy I got this error message which I was not sure about: Traceback (most recent call last): File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 152, in prepare_job job_wrapper.prepare() File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py, line 701, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py, line 2773, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7- macosx-10.6-intel-ucs2.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 83, in respond NotFound: cannot find 'gene' On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: Hi Brad On 04/28/2014 05:26 PM, Bradley Belfiore wrote: So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R '/Users/bbelfio1/Documents/__sample.txt' '04110' 'HSA' I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-. I don't see the word Rscript_wrapper.sh in your line, hence it does not correspond to the command galaxy is executing You provide 3 arguments '/Users/bbelfio1/Documents/__sample.txt', '04110', and 'HSA' However in an earlier mail you mention four arguments: $genedata $pathwayid $species $output Error in grep(species, pathway.id http://pathway.id http://pathway.id) : argument pathway.id http://pathway.id http://pathway.id is missing, with no default Calls: pathview - grep Execution halted As long as you are not sure, whether your script is working on the command line the way you want it to be executed in Galaxy, there is no point in putting it into Galaxy Hans-Rudolf On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch mailto:h...@fmi.ch mailto:h...@fmi.ch wrote: This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output with meaningful arguments On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes
Re: [galaxy-dev] Help with cluster setup
Hi Nate, From your previous email,Job deletion in the pbs runner will be fixed in the next stable release Galaxy.So whether this bug has been fixed in the version of Galaxy( https://bitbucket.org/galaxy/galaxy-dist/get/3b3365a39194.zip)?Thank you very much for your help. Regards,weiyan 2013-08-08 22:58 GMT+08:00 Nate Coraor n...@bx.psu.edu: On Aug 7, 2013, at 9:23 PM, shenwiyn wrote: Yes,and I also have the same confuse about that.Actually when I set server:id in the universe_wsgi.ini as follows for a try,my Galaxy doesn't work with Cluster,if I remove server:id,it work . Hi Shenwiyn, Are you starting all of the servers that you have defined in universe_wsgi.ini? If using run.sh, setting GALAXY_RUN_ALL in the environment will do this for you: http://wiki.galaxyproject.org/Admin/Config/Performance/Scaling [server:node01] use = egg:Paste#http port = 8080 host = 0.0.0.0 use_threadpool = true threadpool_workers = 5 This is my job_conf.xml : ?xml version=1.0? job_conf plugins workers=4 plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=4/ plugin id=pbs type=runner load=galaxy.jobs.runners.pbs:PBSJobRunner workers=8/ /plugins handlers default=batch handler id=node01 tags=batch/ handler id=node02 tags=batch/ /handlers destinations default=regularjobs destination id=local runner=local/ destination id=regularjobs runner=pbs tags=cluster param id=Resource_Listwalltime=24:00:00,nodes=1:ppn=4,mem=10G/param param id=galaxy_external_runjob_scriptscripts/drmaa_external_runner.py/param param id=galaxy_external_killjob_scriptscripts/drmaa_external_killer.py/param param id=galaxy_external_chown_scriptscripts/external_chown_script.py/param /destination /destinations /job_conf The galaxy_external_* options are only supported with the drmaa plugin, and actually only belong in the univese_wsgi.ini for the moment, they have not been migrated to the new-style job configuration. They should also only be used if you are attempting to set up run jobs as the real user job running capabilities. Further more when I want to kill my jobs by clicking Catch(08-08-09-12-39).jpg in galaxy web,the job keeps on running in my background.I do not know how to fix this. Any help on this would be grateful.Thank you very much. Job deletion in the pbs runner was recently broken, but a fix for this bug will be part of the next stable release (on Monday). --nate shenwiyn From: Jurgens de Bruin Date: 2013-08-07 19:55 To: galaxy-dev Subject: [galaxy-dev] Help with cluster setup Hi, This is my first Galaxy installation setup so apologies for stupid questions. I am setting up Galaxy on a Cluster running Torque as the resource manager. I am working through the documentation but I am unclear on some things: Firstly I am unable to find : start_job_runners within the universe_wsgi.ini and I dont want to just add this anywhere - any help on this would be create. Further more this is my job_conf.xml : ?xml version=1.0? !-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -- job_conf plugins plugin id=hpc type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner workers=4/ /plugins handlers !-- Additional job handlers - the id should match the name of a [server:id] in universe_wsgi.ini. handler id=cn01/ handler id=cn02/ /handlers destinations destination id=hpc runner=drmaa/ /destinations /job_conf Does this look meaning full, further more where to I set the additional server:id in the universe_wsgi.ini. As background the cluster has 13 compute nodes and a shared storage array that can be accessed by all nodes in the cluster. Thanks again -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problem with the set_library_permissions function on bioblend
Just retried it on a fresh copy of galaxy-dist (the stable branch of
galaxy-dist now includes this patch) and it worked fine for me. Can
someone else verify? So my best guess is you guys have modified
something in the library code - or you applied that patch but to an
older version of galaxy?
l = gi.libraries.create_library(testlib)
gi.libraries.set_library_permissions( l['id'], access_in=[], modify_in=[],
add_in=[], manage_in=[] )
{u'description': u'', u'deleted': False, u'synopsis': u'',
u'root_folder_id': u'Ff2db41e1fa331b3e', u'model_class': u'Library',
u'id': u'f2db41e1fa331b3e', u'name': u'testlib'}
Sorry I cannot be of more help.
-John
On Wed, Apr 30, 2014 at 7:26 AM, Kevin Muret kmu...@sb-roscoff.fr wrote:
In addition, the content of parser.log file with and without the
modification
With modification :
galaxy.web.framework ERROR 2014-04-30 14:11:52,222 Uncaught exception in
exposed API method:
Traceback (most recent call last):
File
/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/web/framework/__init__.py,
line 199, in decorator
rval = func( self, trans, *args, **kwargs)
File
/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/webapps/galaxy/api/permissions.py,
line 50, in create
item = library.to_dict( view='element', value_mapper={ 'id' :
trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } )
File /w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/model/__init__.py,
line 1960, in to_dict
rval[ 'root_folder_id' ] = 'F' + rval[ 'root_folder_id' ]
TypeError: cannot concatenate 'str' and 'int' objects
Without modification :
galaxy.web.framework ERROR 2014-04-30 14:16:56,853 Uncaught exception in
exposed API method:
Traceback (most recent call last):
File
/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/web/framework/__init__.py,
line 199, in decorator
rval = func( self, trans, *args, **kwargs)
File
/w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/webapps/galaxy/api/permissions.py,
line 50, in create
item = library.to_dict( view='element' )
File /w/galaxy/galaxy4kevin/galaxy-dist/lib/galaxy/model/__init__.py,
line 1960, in to_dict
rval[ 'root_folder_id' ] = 'F' + rval[ 'root_folder_id' ]
TypeError: cannot concatenate 'str' and 'int' objects
Kevin MURET
Intern at Station Biologique de Roscoff
ABiMS platform
___
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
