[galaxy-dev] UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped
Hi all, I think this is the second time I've have the following error on TravisCI (last time I reran a similar failure, and it worked). I've not yet re-run the test so that you can see the full error log: UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped https://travis-ci.org/peterjc/galaxy_blast/builds/60510547 My hunch is this is a race condition, perhaps with the SQLite database? Should I ask TravisCI to re-run the test and confirm this? Peter -- Except from the full log, ... snip ... galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,952 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,957 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,000 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,001 Enabling 'x-forwarded-host' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,002 Enabling 'Request ID' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,046 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.queue_worker INFO 2015-04-29 09:45:14,057 Initalizing Galaxy Queue Worker on sqlalchemy+sqlite:tmp/tmpGyX8vL/tmpTRGC3O/database/universe.sqlite functional_tests.py DEBUG 2015-04-29 09:45:14,089 Attempting to serve app on randomly chosen port: 9572 Error - class 'sqlalchemy.orm.exc.UnmappedClassError': Class 'kombu.transport.sqlalchemy.Message' is not mapped URL: http://localhost:9572/ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in handle_request trans = self.transaction_factory( environ ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 73 in lambda self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 104 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 205 in __init__ self._ensure_valid_session( session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 430 in _ensure_valid_session galaxy_session = self.__create_new_session( prev_galaxy_session, user_for_new_session ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 510 in __create_new_session referer=self.request.headers.get( 'Referer', None ) ) File 'string', line 2 in __init__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 347 in _new_state_if_none File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py', line 747 in __get__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 177 in _state_constructor File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/event/attr.py', line 258 in __call__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2788 in _event_on_first_init File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2684 in configure_mappers File
Re: [galaxy-dev] optional tool arguments
Hi Ryan I guess you can work with filters, see: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set Regards, Hans-Rudolf On 04/28/2015 06:28 PM, Ryan G wrote: Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2 fastq files as input. If 1 file is specified, then 1 output file is created. If 2 inputs are specified, then 2 output files will be created. How do I specify the optional output parameter? I'm using this as my tool description right now: tool id=subsample_fastq name=Random subsample descriptiona fastq file/description command ### Check for optional input file #if strlen($fq2) 0: RandomSubFq -w $readsRequested -i $fq1 -i $fq2 -o $out1 -o $out2 #else: RandomSubFq -w $readsRequested -i $fq1 -o $out1 #end if /command inputs param name=fq1 type=data format=fastq label=FASTQ file (1st of Pair)/ param name=fq2 type=data format=fastq label=FASTQ file (2nd of Pair) optional=true/ param name=readsRequested type=integer min=1 value=10 label=Total number of reads you want from the file/ /inputs outputs data format=fastq name=out1 / data format=fastq name=out2 / /outputs stdio exit_code range=-1 level=fatal description=RandomSubFq failed / /stdio ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] optional tool arguments
Yes, for example: https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/seq_filter_by_id.xml Peter On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Ryan I guess you can work with filters, see: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set Regards, Hans-Rudolf On 04/28/2015 06:28 PM, Ryan G wrote: Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2 fastq files as input. If 1 file is specified, then 1 output file is created. If 2 inputs are specified, then 2 output files will be created. How do I specify the optional output parameter? I'm using this as my tool description right now: tool id=subsample_fastq name=Random subsample descriptiona fastq file/description command ### Check for optional input file #if strlen($fq2) 0: RandomSubFq -w $readsRequested -i $fq1 -i $fq2 -o $out1 -o $out2 #else: RandomSubFq -w $readsRequested -i $fq1 -o $out1 #end if /command inputs param name=fq1 type=data format=fastq label=FASTQ file (1st of Pair)/ param name=fq2 type=data format=fastq label=FASTQ file (2nd of Pair) optional=true/ param name=readsRequested type=integer min=1 value=10 label=Total number of reads you want from the file/ /inputs outputs data format=fastq name=out1 / data format=fastq name=out2 / /outputs stdio exit_code range=-1 level=fatal description=RandomSubFq failed / /stdio ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] follow up question regarding the 'toolform-upgrade'
Hi all We just need some confirmation before we fix our tools: We have several local tools, where the input is a list of (gene)names with the following xml syntax: param name=genenames type=text area=true size=5x20 label=gene names help=(one per line)/ so far this, assuming you enterred: foo bar produced a string like: foo__crcn__bar__crcn__ Now, with toolform-upgrade=True, we get: foo__cn__bar__cn__ (using firefox, with linux, Mac, and Windows) Can anybody confirm this (before we fix all affected tools) Thank you very much for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped
No need, unless it becomes particularly worse after the next attempt to fix it :) On Wed, Apr 29, 2015 at 8:30 AM Peter Cock p.j.a.c...@googlemail.com wrote: Thanks Dannon, Do you want me to send you any future TravisCI cases of this failure? Peter On Wed, Apr 29, 2015 at 1:14 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hi Peter, No need to rerun for my benefit -- it's definitely a race condition that I know about and think I have a fairly good understanding of now. We've tried a few different ideas for fixing it, (obviously none of which have worked, yet), and I've been poking at a new fix this week. -Dannon On Wed, Apr 29, 2015 at 6:53 AM Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I think this is the second time I've have the following error on TravisCI (last time I reran a similar failure, and it worked). I've not yet re-run the test so that you can see the full error log: UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped https://travis-ci.org/peterjc/galaxy_blast/builds/60510547 My hunch is this is a race condition, perhaps with the SQLite database? Should I ask TravisCI to re-run the test and confirm this? Peter -- Except from the full log, ... snip ... galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,952 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,957 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,000 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,001 Enabling 'x-forwarded-host' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,002 Enabling 'Request ID' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,046 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.queue_worker INFO 2015-04-29 09:45:14,057 Initalizing Galaxy Queue Worker on sqlalchemy+sqlite:tmp/tmpGyX8vL/tmpTRGC3O/database/universe.sqlite functional_tests.py DEBUG 2015-04-29 09:45:14,089 Attempting to serve app on randomly chosen port: 9572 Error - class 'sqlalchemy.orm.exc.UnmappedClassError': Class 'kombu.transport.sqlalchemy.Message' is not mapped URL: http://localhost:9572/ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in handle_request trans = self.transaction_factory( environ ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 73 in lambda self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 104 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 205 in __init__ self._ensure_valid_session( session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 430 in _ensure_valid_session galaxy_session = self.__create_new_session( prev_galaxy_session, user_for_new_session ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 510 in __create_new_session referer=self.request.headers.get( 'Referer', None ) ) File 'string', line 2 in __init__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 347 in _new_state_if_none File
Re: [galaxy-dev] follow up question regarding the 'toolform-upgrade'
Hi, I have a related question, does the text-area sanitization differentiate between the different newline formats? Hans-Rudolf can this be your problem? Ciao, Bjoern Am 29.04.2015 um 13:55 schrieb Hans-Rudolf Hotz: Hi all We just need some confirmation before we fix our tools: We have several local tools, where the input is a list of (gene)names with the following xml syntax: param name=genenames type=text area=true size=5x20 label=gene names help=(one per line)/ so far this, assuming you enterred: foo bar produced a string like: foo__crcn__bar__crcn__ Now, with toolform-upgrade=True, we get: foo__cn__bar__cn__ (using firefox, with linux, Mac, and Windows) Can anybody confirm this (before we fix all affected tools) Thank you very much for your help Hans-Rudolf ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped
Hi Peter, No need to rerun for my benefit -- it's definitely a race condition that I know about and think I have a fairly good understanding of now. We've tried a few different ideas for fixing it, (obviously none of which have worked, yet), and I've been poking at a new fix this week. -Dannon On Wed, Apr 29, 2015 at 6:53 AM Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I think this is the second time I've have the following error on TravisCI (last time I reran a similar failure, and it worked). I've not yet re-run the test so that you can see the full error log: UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped https://travis-ci.org/peterjc/galaxy_blast/builds/60510547 My hunch is this is a race condition, perhaps with the SQLite database? Should I ask TravisCI to re-run the test and confirm this? Peter -- Except from the full log, ... snip ... galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,952 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,957 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,000 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,001 Enabling 'x-forwarded-host' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,002 Enabling 'Request ID' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,046 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.queue_worker INFO 2015-04-29 09:45:14,057 Initalizing Galaxy Queue Worker on sqlalchemy+sqlite:tmp/tmpGyX8vL/tmpTRGC3O/database/universe.sqlite functional_tests.py DEBUG 2015-04-29 09:45:14,089 Attempting to serve app on randomly chosen port: 9572 Error - class 'sqlalchemy.orm.exc.UnmappedClassError': Class 'kombu.transport.sqlalchemy.Message' is not mapped URL: http://localhost:9572/ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in handle_request trans = self.transaction_factory( environ ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 73 in lambda self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 104 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 205 in __init__ self._ensure_valid_session( session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 430 in _ensure_valid_session galaxy_session = self.__create_new_session( prev_galaxy_session, user_for_new_session ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 510 in __create_new_session referer=self.request.headers.get( 'Referer', None ) ) File 'string', line 2 in __init__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 347 in _new_state_if_none File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py', line 747 in __get__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 177 in _state_constructor File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/event/attr.py', line 258 in __call__ File
Re: [galaxy-dev] UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped
Thanks Dannon, Do you want me to send you any future TravisCI cases of this failure? Peter On Wed, Apr 29, 2015 at 1:14 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hi Peter, No need to rerun for my benefit -- it's definitely a race condition that I know about and think I have a fairly good understanding of now. We've tried a few different ideas for fixing it, (obviously none of which have worked, yet), and I've been poking at a new fix this week. -Dannon On Wed, Apr 29, 2015 at 6:53 AM Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I think this is the second time I've have the following error on TravisCI (last time I reran a similar failure, and it worked). I've not yet re-run the test so that you can see the full error log: UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped https://travis-ci.org/peterjc/galaxy_blast/builds/60510547 My hunch is this is a race condition, perhaps with the SQLite database? Should I ask TravisCI to re-run the test and confirm this? Peter -- Except from the full log, ... snip ... galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,952 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:13,957 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,000 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,001 Enabling 'x-forwarded-host' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,002 Enabling 'Request ID' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,046 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static galaxy.webapps.galaxy.buildapp DEBUG 2015-04-29 09:45:14,056 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.queue_worker INFO 2015-04-29 09:45:14,057 Initalizing Galaxy Queue Worker on sqlalchemy+sqlite:tmp/tmpGyX8vL/tmpTRGC3O/database/universe.sqlite functional_tests.py DEBUG 2015-04-29 09:45:14,089 Attempting to serve app on randomly chosen port: 9572 Error - class 'sqlalchemy.orm.exc.UnmappedClassError': Class 'kombu.transport.sqlalchemy.Message' is not mapped URL: http://localhost:9572/ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 133 in __call__ return self.handle_request( environ, start_response ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in handle_request trans = self.transaction_factory( environ ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 73 in lambda self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 104 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 205 in __init__ self._ensure_valid_session( session_cookie ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 430 in _ensure_valid_session galaxy_session = self.__create_new_session( prev_galaxy_session, user_for_new_session ) File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/lib/galaxy/web/framework/webapp.py', line 510 in __create_new_session referer=self.request.headers.get( 'Referer', None ) ) File 'string', line 2 in __init__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 347 in _new_state_if_none File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py', line 747 in __get__ File '/home/travis/build/peterjc/galaxy_blast/galaxy-dev/eggs/SQLAlchemy-1.0.1-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/instrumentation.py', line 177 in
Re: [galaxy-dev] PR 149
On Wed, Apr 29, 2015 at 4:40 PM, Roberto Alonso CIPF ralo...@cipf.es wrote: Ok, no problems ;) It is another PR, I think it is useful without the other PR, for example when you map with BWA. The last PR will be like the next step, I mean for example that you split a bam to do some calling or whatever. I think both PR can live independently and together... I don't know if I self-explained well :) Regards Logically splitting BAM files and merging BAM files are separate tasks, and separate pull-requests make sense to me. e.g. Splitting FASTQ files for read mapping, then merging the BAM output. Splitting BAM files for SNP calling, then merging the VCF output. (Splitting BAM files is the more complex case, especially as often you don't really want to touch the BAM file but rather split the processing and exploit the BAI index - e.g. split a BED file of regions instead) Peter ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] PR 149
Ok, no problems ;) It is another PR, I think it is useful without the other PR, for example when you map with BWA. The last PR will be like the next step, I mean for example that you split a bam to do some calling or whatever. I think both PR can live independently and together... I don't know if I self-explained well :) Regards On 29 April 2015 at 17:14, John Chilton jmchil...@gmail.com wrote: No it just slipped through the cracks - sorry about that. I have commented on it now. There was a time when a couple weeks before a first response was the norm :). Does it belong with the bam splitting pull request - is merging useful on its own without the other piece you are working on. -John On Wed, Apr 29, 2015 at 11:04 AM, Roberto Alonso CIPF ralo...@cipf.es wrote: Hello, I created a PR https://github.com/galaxyproject/galaxy/pull/149 dome days ago, but I don't have any feedback yet, is there any problem with it? Is it not interesting for the current Galaxy? didn't the authors realized about it? It would be nice to have some feedback, even if it is not a convenient PR. Thanks so much, Best regards -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralo...@cipf.es ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralo...@cipf.es ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Question about automated cleanup scripts
Hello, I had a quick question about how one of the cleanup scripts works. I was wondering if admin_cleanup_datasets.py will delete old datasets even if they have been shared or published. Thanks for the help -Liam ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Authenticating Against Galaxy from within a tool?
Hi John, Thanks. To elaborate a little more: we have a LabKey Server (web front end for a database) that manages raw files and metadata. The idea is to make a galaxy tool where a user could do thing like query for all genomes from males patients, age x-y, etc. I can use LabKey's APIs to return a list of those files. However, the information at this point is text (basically a list of filepaths). It would be nice to automatically create datasets for those files. Some of the time there's a simple 1:1 between file and the user-facing dataset (like images); however, for genomes we really want to make a paired collection. BioBlend makes it relatively easy to go from filepaths to datasets; however, the authentication issue is what wasnt clear. If there's a more standard path to go from list of files - galaxy dataset I'm all ears. -Ben On Wed, Apr 29, 2015 at 12:13 PM, John Chilton jmchil...@gmail.com wrote: Unofficial way of doing this and the workaround of using configfiles can be found in this thread: http://dev.list.galaxyproject.org/Simple-standard-for-API-use-of-a-global-user-key-that-all-loaded-tools-can-draw-upon-td4665659.html . There is a Trello card outlining platform work that should be done to support this better but we have not made progress on that. I would be interested in your use case. One can dynamically discover datasets with various db keys and build collections composted of dynamically discovered datasets and keys - but there is no way to use the tool xml to dynamically discover a variable number of collections - but it should be supported - as should building a list of paired or lists of lists where the outer list describes the key and the inner the sample. -John On Wed, Apr 29, 2015 at 2:58 PM, Ben Bimber bbim...@gmail.com wrote: Hello, I am new to galaxy. Im trying to write a data input tool wrapper. It will call a script that does a query, produces a list of files, and then the plan is to use the BioBlend API to create datasets/data collections in galaxy. In other words I am making the dataset(s) based on the contents of this file, rather than making a dataset from that file. In my case this file has a pair of columns representing FASTQ files, and I want to create one paired dataset collection in galaxy for each genome. In theory using bioblend to create datasets is easy. However, when I call this as a galaxy tool, I have not found a clean way to pass the credentials to bioblend. BioBlend needs to know the serverURL and either the user's API key or username/password. I think if I poke around $__app__ or $__user__ there's a good change I will find a property with the information I need; however, this has the obvious problem of writing the API key to the log. Is there another way to approach this problem? Thanks in advance for any help, Ben ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] optional tool arguments
Yes it took some experimenting but I finally figured it out. Sent from my iPhone On Apr 29, 2015, at 4:51 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Yes, for example: https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/seq_filter_by_id.xml Peter On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Ryan I guess you can work with filters, see: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set Regards, Hans-Rudolf On 04/28/2015 06:28 PM, Ryan G wrote: Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2 fastq files as input. If 1 file is specified, then 1 output file is created. If 2 inputs are specified, then 2 output files will be created. How do I specify the optional output parameter? I'm using this as my tool description right now: tool id=subsample_fastq name=Random subsample descriptiona fastq file/description command ### Check for optional input file #if strlen($fq2) 0: RandomSubFq -w $readsRequested -i $fq1 -i $fq2 -o $out1 -o $out2 #else: RandomSubFq -w $readsRequested -i $fq1 -o $out1 #end if /command inputs param name=fq1 type=data format=fastq label=FASTQ file (1st of Pair)/ param name=fq2 type=data format=fastq label=FASTQ file (2nd of Pair) optional=true/ param name=readsRequested type=integer min=1 value=10 label=Total number of reads you want from the file/ /inputs outputs data format=fastq name=out1 / data format=fastq name=out2 / /outputs stdio exit_code range=-1 level=fatal description=RandomSubFq failed / /stdio ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Data Libraries
We have 4 different people in our sequencing lab each working on different projects. Once sequencing is done, they want to be able to create a data library specific for that project. Giving them all admin rights is not what we want, but instead giving them the ability to add data libraries so that the PI's and analysts can get access to the data is preferable. Creating one library and allowing them to add subfolders basically forces all the data into 1 library. -- won't work. Having somone with admin rights create a library and give them access to it could work but isn't preferable as that creates unnecessary steps for an admin person that isn't really needed. One only other option is to give them a tool that creates the library for them, but this is a workaround. On Fri, Apr 24, 2015 at 7:28 AM, Nicola Soranzo nsora...@tiscali.it wrote: You may just use a different folder for each project inside a Sequencing library. Would that work? Nicola Il 24.04.2015 13:10 Ryan G ha scritto: This could work. In the long run though, after sequencing for a project, we'd like them people in the sequencing lab to be able to add the data to Galaxy in project specific libraries, without having an admin create a library for them. On Thu, Apr 23, 2015 at 4:56 PM, Martin Čech mar...@bx.psu.edu wrote: Hello Ryan, it is currently not possible to give users rights to create data libraries. However you can create the libraries for them and give them rights to create and manage subfolders (doing the same things but one level below). Would that address your goal? Martin On Thu, Apr 23, 2015 at 4:33 PM Ryan G ngsbioinformat...@gmail.com wrote: Hi all - We are trying to use Galaxy as a mechanism for our sequencing lab to create data libraries for data they generate. I noticed in the docs, only Admins are able to create data libraries. Is there a way to change this? I'd like to give specific users in our group this ability without giving them admin rights. Ryan ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] code tagset in tools
Hi dev, Now that the code tagset is deprecated, how do we replace that functionality. For example the get microbial data tool runs the script listed in the code tagset to load the list of available microbe data when the tool is selected. This doesn't seem to work in the latest stable 15.03.1 or 15.03.2. How do we configure tools like this now? Or is there an updated version of the microbial_import tool? Cheers, Simon. -- Simon Gladman | Bioinformatician Victorian Life Sciences Computation Initiative - LSCC 187 Grattan Street, The University of Melbourne | Victoria 3010 Australia T +61 3 9035 5822 | M 0418 421 077 Mail: simon.glad...@unimelb.edu.au Web: http://www.vlsci.org.au ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] code tagset in tools
On Wed, Apr 29, 2015 at 6:33 AM, Simon Gladman simon.glad...@unimelb.edu.au wrote: Hi dev, Now that the code tagset is deprecated, how do we replace that functionality. For example the get microbial data tool runs the script listed in the code tagset to load the list of available microbe data when the tool is selected. This doesn't seem to work in the latest stable 15.03.1 or 15.03.2. How do we configure tools like this now? Or is there an updated version of the microbial_import tool? Cheers, Simon. Good question Simon. I am still using code for advanced parameter validation, e.g. https://github.com/peterjc/pico_galaxy/blob/64aecfa6041b3b7fe2c70a30236a7aa15e650523/tools/mira4_assembler/mira4_de_novo.xml i.e. Validation before the job gets submitted to the cluster or run. If the code tag suddenly goes away, my tool will still work but would be a little less user friendly (some errors would only be spotted after the tool starts running). Peter ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed
You are correct. It's always passing even when it fails. There was nothing in the docs to indicate a pass. Sent from my iPhone On Apr 28, 2015, at 3:44 PM, John Chilton jmchil...@gmail.com wrote: I feel like that stdio tag is going to cause it to always pass - even if the exit code is not 0. Am I wrong? I like: stdio exit_code range=1: / /stdio myself. Björn Grüning uses - stdio exit_code range=1: / exit_code range=:-1 / regex match=Error: / regex match=Exception: / /stdio which is a popular choice. As a heads up for people reading discussion in the future - starting in 15.05 - you will be able to just add detect_errors=exit_code on the command tag to get a more sensible default behavior. https://github.com/galaxyproject/galaxy/pull/117 -John On Tue, Apr 28, 2015 at 12:12 PM, Ryan G ngsbioinformat...@gmail.com wrote: stdio exit_code range=-1 level=fatal description=RandomSubFq failed / /stdio this works. Thanks. On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker dannon.ba...@gmail.com wrote: Like Peter mentions, we did this because historically not all tools used (still don't, I guess) exit codes correctly. If yours does, you can set exit_code tags and everything should work. On Tue, Apr 28, 2015 at 11:47 AM Ryan G ngsbioinformat...@gmail.com wrote: ok, thanks. Let me look at this. When I look at the information about the tool, Galaxy does see the exit code is 0, which I think would be sufficient to know the tool ran correctly. On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock p.j.a.c...@googlemail.com wrote: You probably need to set the stdio tag, since due to a historical design choice by default any output on stderr is treated as an error. See: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter On Tue, Apr 28, 2015 at 4:41 PM, Ryan G ngsbioinformat...@gmail.com wrote: Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed. I checked the output file the tools create, and it succeeded. How do I tell Galaxy that a tool it ran was successful? Is it something in my XML file? The tool is outputting some info to stderr. Could this be why? ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] code tagset in tools
Hi Dan, Thanks for the reply and the suggestions. I think the data libraries would work much better than the get_microbial_data tool as then it would be more easily kept up to date. Cheers, Simon. On 30 April 2015 at 01:01, Daniel Blankenberg d...@bx.psu.edu wrote: The code tag won’t be going away any time soon, but in many cases there are other ways to do what this tag does, using the built-in dynamic options (in particular, currently for tab-delimited files), that are much preferred. So it is deprecated, and it should be used sparingly, but there are times when there isn’t a better way for tools to dynamically build their options without using a code file. In the case of the get microbial data tool, if it was working prior to 15.03, it should still be working, afaik we haven’t changed the handling of these recently (with the exception of not loading them inside of a ToolShed application instance). Its been a while since I’ve played with that specific tool (and we deprecated it ourselves and removed it from main), so I can’t confirm off-the-cuff whether it should still be working or not. If something really did break with respect to the code files, we should take a look though. I think using a Data Library is the perfect replacement for for the microbial import tool, and would cause less file duplication when used. But what exactly is no longer working? Thanks for using Galaxy, Dan On Apr 29, 2015, at 10:38 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Apr 29, 2015 at 6:33 AM, Simon Gladman simon.glad...@unimelb.edu.au wrote: Hi dev, Now that the code tagset is deprecated, how do we replace that functionality. For example the get microbial data tool runs the script listed in the code tagset to load the list of available microbe data when the tool is selected. This doesn't seem to work in the latest stable 15.03.1 or 15.03.2. How do we configure tools like this now? Or is there an updated version of the microbial_import tool? Cheers, Simon. Good question Simon. I am still using code for advanced parameter validation, e.g. https://github.com/peterjc/pico_galaxy/blob/64aecfa6041b3b7fe2c70a30236a7aa15e650523/tools/mira4_assembler/mira4_de_novo.xml i.e. Validation before the job gets submitted to the cluster or run. If the code tag suddenly goes away, my tool will still work but would be a little less user friendly (some errors would only be spotted after the tool starts running). Peter ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Simon Gladman | Bioinformatician Victorian Life Sciences Computation Initiative - LSCC 187 Grattan Street, The University of Melbourne | Victoria 3010 Australia T +61 3 9035 5822 | M 0418 421 077 Mail: simon.glad...@unimelb.edu.au Web: http://www.vlsci.org.au ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] PR 149
Hello, I created a PR https://github.com/galaxyproject/galaxy/pull/149 dome days ago, but I don't have any feedback yet, is there any problem with it? Is it not interesting for the current Galaxy? didn't the authors realized about it? It would be nice to have some feedback, even if it is not a convenient PR. Thanks so much, Best regards -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralo...@cipf.es ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] code tagset in tools
The code tag won’t be going away any time soon, but in many cases there are other ways to do what this tag does, using the built-in dynamic options (in particular, currently for tab-delimited files), that are much preferred. So it is deprecated, and it should be used sparingly, but there are times when there isn’t a better way for tools to dynamically build their options without using a code file. In the case of the get microbial data tool, if it was working prior to 15.03, it should still be working, afaik we haven’t changed the handling of these recently (with the exception of not loading them inside of a ToolShed application instance). Its been a while since I’ve played with that specific tool (and we deprecated it ourselves and removed it from main), so I can’t confirm off-the-cuff whether it should still be working or not. If something really did break with respect to the code files, we should take a look though. I think using a Data Library is the perfect replacement for for the microbial import tool, and would cause less file duplication when used. But what exactly is no longer working? Thanks for using Galaxy, Dan On Apr 29, 2015, at 10:38 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Apr 29, 2015 at 6:33 AM, Simon Gladman simon.glad...@unimelb.edu.au wrote: Hi dev, Now that the code tagset is deprecated, how do we replace that functionality. For example the get microbial data tool runs the script listed in the code tagset to load the list of available microbe data when the tool is selected. This doesn't seem to work in the latest stable 15.03.1 or 15.03.2. How do we configure tools like this now? Or is there an updated version of the microbial_import tool? Cheers, Simon. Good question Simon. I am still using code for advanced parameter validation, e.g. https://github.com/peterjc/pico_galaxy/blob/64aecfa6041b3b7fe2c70a30236a7aa15e650523/tools/mira4_assembler/mira4_de_novo.xml i.e. Validation before the job gets submitted to the cluster or run. If the code tag suddenly goes away, my tool will still work but would be a little less user friendly (some errors would only be spotted after the tool starts running). Peter ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
