[galaxy-dev] output file
Hi, After execution, my tool created many files in a directory , how can I to find this directory? command: bash mytool.sh $input ___ 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/
Re: [galaxy-dev] refresh_on_change is broken?
Hi, The Extract GFF Features doesn't use dynamic options and I don't think that's really the question here. Let me give an example of something that I do. I have the user select a file after which I, using dynamic_options, extract the column names and present those to the user with a select input parameter. With the selected column name I then present a new select input parameter with all the unique values of the selected column. To get this to work I am now using three pages since it is really dynamic, thus after each parameter (that uses dynamic_options) I need to make a new page to use the selected item, thus: page param name=input_dataset type=data format=tabular, txt label=Input dataset / /page page param name=colfilter type=select multiple=False label=Select Filtering Column dynamic_options=get_columns( input_dataset ) / /page page param name=filter_values type=select multiple=True label=Select Filtering Values dynamic_options=get_filter( input_dataset, colfilter, 2 ) / /page This works fine, however it requires three pages which is deprecated. The documentation says 'use refresh_on_change' which is an undocumented feature (please (please!!) fix this!) with no examples anywhere on how to replace common page usage. So given above example (which is similar to what the original requester asked), where to place the refresh_on_change option to get it working? I've of course tried to place it within both dynamic_option parameters but this doesn't update the 'filter_values' parameter depending on the 'colfilter' parameter.. Kind regards, Marcel http://lists.bx.psu.edu/ /quote Quoted from: http://gmod.827538.n3.nabble.com/refresh-on-change-is-broken-tp3786745p3852979.html -- Message: 12 Date: Fri, 23 Mar 2012 18:41:11 -0400 From: Jeremy Goecks jeremy.goe...@emory.edu To: Greg Von Kuster g...@bx.psu.edu Cc: Gubian, Sylvain sylvain.gub...@pmi.com, Galaxy Dev galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] refresh_on_change is broken? Message-ID: 302260d0-f8b3-4c09-ad59-aeb6239c8...@emory.edu Content-Type: text/plain; charset=us-ascii A final pointer: to see tools that use dynamic options, take a look at Extract GFF features and Filter GFF dataset by feature count Good luck, J. De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. ___ 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/
Re: [galaxy-dev] galaxy cluster integration
We are using PBS locally and had our cluster admin set this up, but I think the same principle applies across most job runners/mgrs. As Peter mentioned, there should be a way for cluster admin to add your server as an allowed submitting host, the PBS variant is here: http://www.clusterresources.com/torquedocs/2.1jobsubmission.shtml#submitaccess There also may be additional tweaking required due to firewalls, etc. After that, run some simple job submission tests (we ran a simple 'sleep 60') from your server to check whether you can submit jobs, see submitted job status, etc. I found it helped when debugging to log in on both Galaxy server and cluster sides, and if the cluster admin allows it monitor the job manager logs on the cluster side if you run into problems (we found this very handy when debugging local LDAP issues). chris On May 2, 2012, at 4:16 PM, Anne Pajon wrote: Yes we do have an LSF cluster. Thanks indeed for all the information, Peter. I'll contact our cluster administrator tomorrow and keep you posted on my progress. Kind regards, Anne. On 2 May 2012, at 22:07, Peter Cock wrote: On Wed, May 2, 2012 at 9:58 PM, Anne Pajon anne.pa...@cancer.org.uk wrote: Hi Peter, Thanks for the clarification, it is really helpful. Would you mind sharing what needs to be done in term of configuration and instalation to transform the galaxy server into a submitting job to the cluster? Thanks. You said you have an LSF cluster - so I have no idea, sorry :( We're using SGE here. I'm presuming similar concepts apply - in our case a key step was getting qsub/qstat/qdel to work from the Galaxy server as well as the cluster head node - which required our cluster administrator to setup our Galaxy server as an SGE submit node. Regards, Peter -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pa...@cancer.org.uk | +44 (0)7958 511 353 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ 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/ ___ 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/
Re: [galaxy-dev] refresh_on_change is broken?
Let me give an example of something that I do. I have the user select a file after which I, using dynamic_options, extract the column names and present those to the user with a select input parameter. With the selected column name I then present a new select input parameter with all the unique values of the selected column. To get this to work I am now using three pages since it is really dynamic, thus after each parameter (that uses dynamic_options) I need to make a new page to use the selected item, thus: page param name=input_dataset type=data format=tabular, txt label=Input dataset / /page page param name=colfilter type=select multiple=False label=Select Filtering Column dynamic_options=get_columns( input_dataset ) / /page page param name=filter_values type=select multiple=True label=Select Filtering Values dynamic_options=get_filter( input_dataset, colfilter, 2 ) / /page This works fine, however it requires three pages which is deprecated. The documentation says 'use refresh_on_change' which is an undocumented feature (please (please!!) fix this!) with no examples anywhere on how to replace common page usage. refresh_on_change is not meant to be used explicitly in a tool's config file; it is an internal feature used by Galaxy to refresh pages as necessary, such as for conditionals. Also, dynamic_options has been deprecated in favor of the options tag. So given above example (which is similar to what the original requester asked), where to place the refresh_on_change option to get it working? If I'm reading your code right, this should be possible using the options tag only. First, select the dataset and then use something like for subsequent parameters: options from_dataset=input_dataset column name=name index=0/ column name=value index=0/ filter type=unique_value name=unique column=0/ /options Best, J. ___ 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/
[galaxy-dev] Migrate history datasets to new database
Hello all, I recently tried moving from a tarball install of Galaxy to a Mercurial managed one, and in the process something went wrong with the database upgrade. I had intended to install the Mercurial-based Galaxy separately (though on the same machine) and then move it to production once it was working but it installed in-place over the current database while it was still completely active/up and running. That broke my existing Galaxy install and I had to move to the new install immediately. I recall having to run the Mercurial install's run.sh script multiple times though because the upgrade sequence (looked like 87-88, 88-89, etc. as it progressed) did not complete all the way the first time. I also ran it as root when I probably should have done it as our galaxy user. Long story short now I cannot log in to Galaxy even though Galaxy recognizes correct credentials from the database. My debugging so far has not yielded any results. At this point after a week of unsuccessful attempts to repair the existing install I just want to create a fresh database and migrate over our users' history and dataset (and possibly login credentials) information stored in the database to the new one, if at all possible. Could someone give me any guidance as to how to do that, and which table files (MYI, MYD, etc.) that I should copy over into the new mysql database to make that happen? P.S. I do have to thank Dannon Baker for helping me so far through private email correspondence to try to figure out what went wrong with the current install. However I'm not having any breakthroughs and our local Galaxy mirror has been down for over a week now and I just want to start fresh and migrate over critical data if possible. Thanks for your help, Josh Nielsen ___ 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/
[galaxy-dev] Error when exporting history to file
Hi all, I get the following error when I try to export a specific history to file: 10.1.5.190 - - [07/May/2012:18:01:08 +0200] GET /history/export_archive HTTP/1.1 500 - http://galaxy.immunbio.mpg.de/; Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/2008 Fedora/3.6.24-1.fc14 Firefox/3.6.24 Error - type 'exceptions.TypeError': galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError: galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file... Any help is greatly appreciated! Best regards, Sarah ___ 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/
Re: [galaxy-dev] Error when exporting history to file
Sarah, What tool was used to create the problematic dataset? Thanks, J. On May 7, 2012, at 12:17 PM, Sarah Diehl wrote: Hi all, I get the following error when I try to export a specific history to file: 10.1.5.190 - - [07/May/2012:18:01:08 +0200] GET /history/export_archive HTTP/1.1 500 - http://galaxy.immunbio.mpg.de/; Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/2008 Fedora/3.6.24-1.fc14 Firefox/3.6.24 Error - type 'exceptions.TypeError': galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError: galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file... Any help is greatly appreciated! Best regards, Sarah ___ 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/ ___ 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/
[galaxy-dev] send data error
Hi, We just installed a galaxy server and are doing the tools testing right now. When we were testing the Send Data tool, we encountered an error as below. Error executing tool: 302 Found The resource was found at /tool_runner/redirect?redirect_url=http%3A%2F%2Fepigraph.mpi-inf.mpg.de%2FWebGRAPH_Public_Test%2Ffaces%2FDataImport.jsp%3FDATA_URL%3Dhttps%3A%2F%2Fgalaxy.indiana.edu%2Fdatasets%2F6%2Fdisplay%26INFO%3D%26GENOME%3Dhg18%26NAME%3DConvert+genome+coordinates+on+data+4+%5B+UNMAPPED+COORDINATES+%5D%26USERNAME%3Dlewu%40indiana.edu%26GALAXY_URL%3Dhttps%3A%2F%2Fgalaxy.indiana.edu%2Ftool_runner%3Ftool_id%3Depigraph_import Does this mean the redirect URL is wrong or something else? Can someone help us to solve this problem? Thanks a lot. Best LW___ 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/
