- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Tool param type "library_data" (Dooley, Damion)
by Dooley, Damion 20 Apr '15

20 Apr '15

I was successful getting library dataset selection and form submission to happen within tool form tool form input <param type="library_data" ...> - Yay! But it appears one last fix (besides the "url: "/visualization/list_libraries",' bug) is needed to enable history tool item to be RERUN. So if a galaxy dev can tackle this, great! Otherwise I'll have to drop this approach :<( ***************** For others who may need... tool form's param: <param name="library_datasets" type="library_data" label="Reference Bin file" help="Select one reference bin at a time from the popup window's Reference Bin library."/> <command> tag contents.... #if $library_datasets -B " #for $i, $dataset in enumerate($library_datasets) #$dataset.get_file_name() $dataset.id #end for " #end if Successfully submits either the full file path of selected dataset, or its id. ***************** However trying to rerun this history tool item gets us an error (not related to the above <command> contents): Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'int' object has no attribute 'id' .... Module galaxy.tools.parameters.basic:146 in value_to_basic view >> return self.to_string( value, app ) Module galaxy.tools.parameters.basic:2406 in to_string app <galaxy.app.UniverseApplication object at 0x59a0710> ldda 331 self <galaxy.tools.parameters.basic.LibraryDatasetToolParameter object at 0x7fced01d2090> value [331] >> return [ldda.id for ldda in value] AttributeError: 'int' object has no attribute 'id' which is in /lib/galaxy/tools/parameters/basic.py: class LibraryDatasetToolParameter( ToolParameter ): """ Parameter that lets users select a LDDA from a modal window, then use it within the wrapper. """ ... def to_string( self, value, app ): if not value: return value return [ldda.id for ldda in value] "Value" is getting an array of dataset ids, whereas this method is expecting value to be a list of dataset objects. I tried changing ldda.id to just "id" but found other parts of LibraryDatasetTool code were broken as they too were expecting an object. Maybe this is related to the tool job's history detail link showing "Reference Bin file" as a string label of an object?: Input Parameter Value Note for rerun BLAST results as XML 240: megablast Pasted Entry vs 16SMicrobial.fasta Reference Bin file [<galaxy.model.LibraryDatasetDatasetAssociation object at 0x7fcee04d4350>] Tabular Report Column Labels Short name HTML Report template templates.html_report ******************************** The other bug: 2) Tool_form.mako has a hardcoded url that doesn't work for galaxy installs that have a prefix so that needs adjustment: $(".add-librarydataset").click(function() { var link = $(this); $.ajax({ url: "/visualization/list_libraries",

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April GalaxyAdmins Meetup: Video and Slides are now available
by Dave Clements 20 Apr '15

20 Apr '15

Hi all, Slides from both talks and video of the whole meetup are now available at https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_04_16 Many thanks to Carrie and Sam for presenting. See you at the next meetup June 18! Dave C On Thu, Apr 16, 2015 at 7:34 AM, Dave Clements <clements(a)galaxyproject.org> wrote: > Hello all, > > GalaxyAdmins is starting in about 25 minutes. The room is here: > > https://connect.johnshopkins.edu/galaxyadmins201504/ > > It takes a few minutes to navigate through Flash, so connecting a few > minutes early is encouraged. > > Thanks, > > Dave C > > > > On Wed, Apr 15, 2015 at 9:14 AM, Dave Clements <clements(a)galaxyproject.org > > wrote: > >> Hello all, >> >> Just a reminder that the April GalaxyAdmins online meetup is tomorrow, >> Thursday, at 5pm Central European Summer Time. See >> https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_04_16 >> for details. A link to the meetup will be posted about an hour before the >> meetup. >> >> Thanks, >> >> Dave C >> >> On Thu, Apr 9, 2015 at 12:58 PM, Dave Clements < >> clements(a)galaxyproject.org> wrote: >> >>> Hello all, >>> >>> The April 2015 GalaxyAdmins meetup >>> <https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_04_16> >>> will be held online on Thursday, 16 April (a week from today). We'll meet >>> at 5pm Central European Summer Time (see your local time >>> <http://bit.ly/1EFUf0M>). >>> >>> Carrie Ganote <http://www.researchgate.net/profile/Carrie_Ganote> from >>> the National Center for Genome Analysis Support (NCGAS) >>> <http://ncgas.org/> and Pervasive Technology Institute >>> <http://pti.iu.edu/> at Indiana University will talk about her Galaxy >>> work with Trinity, IU Galaxy, and the Open Science Grid. And Sam >>> Guerler <https://wiki.galaxyproject.org/guerler> of the Galaxy Team >>> will also discuss recent work to update Galaxy's tool forms. >>> >>> GalaxyAdmins <https://wiki.galaxyproject.org/Community/GalaxyAdmins> is >>> a discussion group for Galaxy community members who are responsible for >>> Galaxy installations. Please see the meetup page ( >>> http://bit.ly/gxyadm201504) for more details. >>> >>> Hope to see (hear?) you there, >>> >>> Dave C (channeling Hans-Rudolf Hotz) >>> >>> -- >>> http://galaxyproject.org/ >>> http://getgalaxy.org/ >>> http://usegalaxy.org/ >>> https://wiki.galaxyproject.org/ >>> >> >> >> >> -- >> http://galaxyproject.org/ >> http://getgalaxy.org/ >> http://usegalaxy.org/ >> https://wiki.galaxyproject.org/ >> > > > > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > https://wiki.galaxyproject.org/ > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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GCC2015 Oral Presentation Abstract Submission closes 20 April
by Dave Clements 20 Apr '15

20 Apr '15

Hello all, Just a reminder that oral presentation abstract submission for GCC2015 closes on Monday, 20 April, 5 days from now. Poster submission closes 1 May. See http://gcc2015.tsl.ac.uk/Abstracts for more. The 2015 Galaxy Community Conference is an opportunity to share your work with 200+ other researchers working in data-intensive biology. GCC2015 features 2 days of (2 different) hackathons, 2 days of training, and 2 days of meeting, posters, presentations, birds of a feather, and networking. See http://gcc2015.tsl.ac.uk/ for more on GCC2015. Looking forward to seeing you in July in Norwich! Dave C. On Wed, Feb 25, 2015 at 12:04 AM, Dave Clements <clements(a)galaxyproject.org> wrote: > Hello all, > > *We are pleased to announce that abstract submission for Oral and Poster > Presentations <http://gcc2015.tsl.ac.uk/Abstracts> at the 2015 Galaxy > Community Conference (GCC2015) <http://gcc2015.tsl.ac.uk/> is now open.* > > Abstract submission <http://gcc2015.tsl.ac.uk/Abstracts> for oral > presentations closes 10 April, and poster submission closes 1 May. Poster > authors will be notified of acceptance status within two weeks of > submission, while oral presentation authors will be notified no later than > 24 April. *Please consider presenting your work. If you are dealing with > big biological data, then this meeting wants to hear about it.* > > *About GCC2015* > > GCC2015 <http://gcc2015.tsl.ac.uk/> is hosted by The Sainsbury Lab > <http://www.tsl.ac.uk/>, in Norwich, United Kingdom > <http://www.visitnorwich.co.uk/>, in July 2015. GCC has been expanded > this year and will now offer two hackathons, two Training Days, and a two > day conference <http://gcc2015.tsl.ac.uk/programme/>. The Training Days > <http://gcc2015.tsl.ac.uk/training-day/> cover 15 different topics > spanning the full Galactic spectrum of topics. *Take a look > <http://gcc2015.tsl.ac.uk/programme/>.* > > Thanks, > > GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers/> > > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > https://wiki.galaxyproject.org/ > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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anybody seen this class of error before?
by Langhorst, Brad 20 Apr '15

20 Apr '15

InvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: Class 'kombu.transport.sqlalchemy.Message' is not mapped galaxy.jobs.handler ERROR 2015-04-19 14:46:00,794 Exception in monitor_step Traceback (most recent call last): File "/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 177, in __monitor self.__monitor_step() File "/mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 229, in __monitor_step jobs_to_check = self.sa_session.query(model.Job).enable_eagerloads(False) \ File "/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/scoping.py", line 150, in do return getattr(self.registry(), name)(*args, **kwargs) File "/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/session.py", line 1165, in query return self._query_cls(entities, self, **kwargs) File "/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py", line 108, in __init__ self._set_entities(entities) File "/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py", line 118, in _set_entities self._set_entity_selectables(self._entities) File "/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py", line 151, in _set_entity_selectables ent.setup_entity(*d[entity]) File "/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py", line 3036, in setup_entity self._with_polymorphic = ext_info.with_polymorphic_mappers File "/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/util/langhelpers.py", line 725, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/mapper.py", line 1877, in _with_polymorphic_mappers configure_mappers() File "/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/mapper.py", line 2586, in configure_mappers raise e Once this error occurs, no more jobs execute on the cluster. Restarting the handler seems to get things moving again, but I’d like to find the source of the failure. Any ideas? Brad -- Brad Langhorst, Ph.D. Applications and Product Development Scientist

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Error generating Picard indexes when using data_manager_gatk_picard_index_builder from the main tool shed
by Paulo Silva 17 Apr '15

17 Apr '15

Hello all Galaxy devs, I’ve come across (what seems to be) a Galaxy bug (or rather, tool-shed bug) when I run the data manager data_manager_gatk_picard_index_builder (rev. a15709ad26ea) from the Galaxy main tool shed repo on a clean Galaxy install. Installation goes fine - when I install this data manager, all dependencies are correctly installed: package_picard_1_56_0 (rev. 99a28567c3a3) and package_samtools_0_1_18 (rev. 171cd8bc208d). After installation, I go to Admin -> Manage local data (beta) -> Run Data Manager Tools, click “Generate GATK-sorted Picard indexes” and the data manager form is displayed. I select the reference genome (either hg19 or hg38 - installed with data_manager_fetch_genome_dbkeys_all_fasta from the main tool shed, rev. bca4c608408c - working fine with other tools including bowtie2 and trackster), enter “hg19” both “Name of sequence” and “ID for sequence” fields, and click “Execute”. The indexing job is added to the queue, but when I go to view data manager jobs for this data manager, I see it stopped with the following error: Traceback (most recent call last): File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea/data_manager_gatk_picard_index_builder/data_manager/data_manager_gatk_picard_index_builder.py", line 179, in <module> if __name__ == "__main__": main() File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea/data_manager_gatk_picard_index_builder/data_manager/data_manager_gatk_picard_index_builder.py", line 162, in main raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) ) Exception: "None" is not a valid dbkey. You must specify a valid dbkey. Inspecting galaxy.log doesn’t reveal anything relevant (at least for me - which is why I need your help!): galaxy.jobs DEBUG 2015-04-17 11:13:23,031 (63) Working directory for job is: /home/galaxy/galaxy-dist/database/job_working_directory/000/63 galaxy.jobs.handler DEBUG 2015-04-17 11:13:23,044 (63) Dispatching to local runner 192.168.2.74 - - [17/Apr/2015:11:13:22 +0100] "POST /api/tools HTTP/1.1" 200 - "http://192.168.2.221:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepo…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_2) AppleWebKit/600.4.10 (KHTML, like Gecko) Version/8.0.4 Safari/600.4.10" galaxy.jobs DEBUG 2015-04-17 11:13:23,168 (63) Persisting job destination (destination id: local) galaxy.jobs.handler INFO 2015-04-17 11:13:23,212 (63) Job dispatched galaxy.tools.deps DEBUG 2015-04-17 11:13:23,393 Building dependency shell command for dependency 'samtools' galaxy.tools.deps DEBUG 2015-04-17 11:13:23,395 Building dependency shell command for dependency 'picard' galaxy.jobs.runners DEBUG 2015-04-17 11:13:23,475 (63) command is: PACKAGE_BASE=/home/galaxy/tool-deps/samtools/0.1.18/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea; export PACKAGE_BASE; . /home/galaxy/tool-deps/samtools/0.1.18/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea/env.sh; PACKAGE_BASE=/home/galaxy/tool-deps/picard/1.56.0/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea; export PACKAGE_BASE; . /home/galaxy/tool-deps/picard/1.56.0/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea/env.sh; python /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/a15709ad26ea/data_manager_gatk_picard_index_builder/data_manager/data_manager_gatk_picard_index_builder.py "/home/galaxy/galaxy-dist/database/files/000/dataset_70.dat" \ --jar "$JAVA_JAR_PATH/CreateSequenceDictionary.jar" \ --fasta_filename "/home/galaxy/galaxy-dist/tool-data/hg19/seq/hg19.fa" \ --fasta_dbkey "hg19" \ --fasta_description "Human, Feb. 2009, GRCh37/hg19" \ --data_table_name "gatk_picard_indexes"; return_code=$?; python /home/galaxy/galaxy-dist/database/job_working_directory/000/63/set_metadata_Ts4xSd.py /home/galaxy/galaxy-dist/database/tmp/tmpfomc7m /home/galaxy/galaxy-dist/database/job_working_directory/000/63/galaxy.json /home/galaxy/galaxy-dist/database/job_working_directory/000/63/metadata_in_HistoryDatasetAssociation_70_Lkhynl,/home/galaxy/galaxy-dist/database/job_working_directory/000/63/metadata_kwds_HistoryDatasetAssociation_70_IuPBQs,/home/galaxy/galaxy-dist/database/job_working_directory/000/63/metadata_out_HistoryDatasetAssociation_70_uuRnIn,/home/galaxy/galaxy-dist/database/job_working_directory/000/63/metadata_results_HistoryDatasetAssociation_70_aVp4XH,/home/galaxy/galaxy-dist/database/files/000/dataset_70.dat,/home/galaxy/galaxy-dist/database/job_working_directory/000/63/metadata_override_HistoryDatasetAssociation_70_hXaBQB; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2015-04-17 11:13:23,476 (63) executing job script: /home/galaxy/galaxy-dist/database/job_working_directory/000/63/galaxy_63.sh galaxy.jobs DEBUG 2015-04-17 11:13:23,526 (63) Persisting job destination (destination id: local) galaxy.jobs.runners.local DEBUG 2015-04-17 11:13:24,976 execution finished: /home/galaxy/galaxy-dist/database/job_working_directory/000/63/galaxy_63.sh galaxy.jobs DEBUG 2015-04-17 11:13:25,054 setting dataset state to ERROR galaxy.jobs DEBUG 2015-04-17 11:13:25,122 job 63 ended galaxy.datatypes.metadata DEBUG 2015-04-17 11:13:25,123 Cleaning up external metadata files Some more system details: Galaxy version: latest_15.03, running on Ubuntu 14.04.2 LTS Java: 1.8.0_45-b14 from the webupd8 Ubuntu repo. Using Postresql locally, everything else local too. Cloned from the Bitbucket repo (in case this matters). Can anyone shed some light on this? In the traceback log above it seems options.fasta_dbkey is being set to “None” rather than “hg19” but I am not sure how to solve this, or if this is indeed the problem. Thank you in advance! All the best, -- Paulo ____________________________________________________________ Paulo Filipe Silva | PhD, Biology | MSc, Bioinformatics Bioinformatician @ CGPP - Centre for Predictive and Preventive Genetics http://www.cgpp.eu <http://www.cgpp.eu/> IBMC - Institute for Molecular and Cell Biology Rua do Campo Alegre, 823 4150-180 Porto, Portugal E-mail: paulo.silva(a)ibmc.up.pt <mailto:paulo.silva@ibmc.up.pt> Telephone: +351 22 607 49 42 ext 2811 Fax: +351 22 600 29 23

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metadata in parallelization
by Roberto Alonso CIPF 17 Apr '15

17 Apr '15

Hello, I am writing some code to enable parallelization for some tool wrappers. First, I did it for simple bwa wrapper, but now I am modifying toolshed.g2.bx.psu.edu/repos/devteam/bwa/c71dd035971e/bwa/bwa-mem.xml to check if the code would work with this wrapper. So, I wrote some code that I thing was necessary in order to merge some bam and I added the parallelism tag (in bold) to the config file: <tool id="bwa_mem" name="BWA-MEM" version="0.1"> <macros> <import>bwa_macros.xml</import> </macros> <requirements> <requirement type="package" version="0.7.10.039ea20639">bwa</requirement> <requirement type="package" version="1.1">samtools</requirement> </requirements> <description>- map medium and long reads (> 100 bp) against reference genome</description> <parallelism method="multi" split_size="3" shared_inputs="ref_file" split_mode="number_of_parts" merge_outputs="bam_output" split_inputs="fastq_input1,fastq_input2" ></parallelism> <command> ... So, everything works well, and the resulting bam from parallelization mode and without the parallelization mode is the same but the Galaxy log throws an error regarding metadata, it says something like this: galaxy.jobs.splitters.multi DEBUG 2015-04-17 09:54:58,335 merge finished: /home/ralonso/galaxy/database/files/000/dataset_198.dat galaxy.jobs.runners.tasks DEBUG 2015-04-17 09:54:58,473 executing external set_meta script for job 200: python /home/ralonso/galaxy/database/tmp/set_metadata_E5fGIE.py /home/ralonso/galaxy/database/tmp/tmpHS8Byo /home/ralonso/galaxy/database/job_working_directory/000/200/galaxy.json /home/ralonso/galaxy/database/tmp/metadata_in_HistoryDatasetAssociation_198_yOGiQG,/home/ralonso/galaxy/database/tmp/metadata_kwds_HistoryDatasetAssociation_198_nAsQoq,/home/ralonso/galaxy/database/tmp/metadata_out_HistoryDatasetAssociation_198_I_cLs4,/home/ralonso/galaxy/database/tmp/metadata_results_HistoryDatasetAssociation_198_qhjzoV,/home/ralonso/galaxy/database/files/000/dataset_198.dat,/home/ralonso/galaxy/database/tmp/metadata_override_HistoryDatasetAssociation_198_ScKLqH Traceback (most recent call last): File "/home/ralonso/galaxy/database/tmp/set_metadata_E5fGIE.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() ImportError: No module named galaxy_ext.metadata.set_metadata galaxy.jobs.runners.tasks DEBUG 2015-04-17 09:54:58,624 execution of external set_meta finished for job 200 galaxy.datatypes.metadata DEBUG 2015-04-17 09:54:58,714 setting metadata externally failed for HistoryDatasetAssociation 198: External set_meta() not called When using no parallelization mode, there is no problem, also because Galaxy doesn't go through this part of code, I mean it doesn't execute this. I see that Galaxy have to do something with metada attributes, but what is t trying to do? is there any way to solve this? Thank you very much 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: ralonso(a)cipf.es

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Difference between GitHub and Mercurial Galaxy download...
by Asma Riyaz 16 Apr '15

16 Apr '15

Hi, Is there a difference between the github and mercurial galaxy downloads? Is there one preferred over another? The galaxy website asks to do a Github download and many other places including the GMOD tutorial held last summer on Galaxy suggested a mercurial one? Kindly advice. Thank you, Asma

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substitution of special characters in arguments of galaxy tools
by Wang, Yu 16 Apr '15

16 Apr '15

Dear galaxy developers, Galaxy seems to substitute special characters when it passes arguments to its tools (e.g. the content of input fields of type 'text'). In general, this is useful. However, '%' is substituted by 'X', i.e. the substitution is not invertible which can be a real show stopper. Is there some way to change this substitution or switch it of completely? Cheers, Yu di29her wang(a)lrz.de<mailto:wang@lrz.de>

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Older galaxy I'm keeping alive by drip feed, has problem restarting when I turn debug off.
by Dooley, Damion 16 Apr '15

16 Apr '15

I have an OLDER Galaxy install I was going to fade out. In meantime I saw that its debug flag should be turned off, so I did. But when it restarted it complained in the history tab with a server error. I put debug back into config and it runs fine. I haven't changed anything recently on it. Wondering if there is a simple remedy? Details below. Thanks, Damion ********************************************************* Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) And indeed, after the startup log message... serving on http://127.0.0.1:8080 There is an error that seems to be triggered when A GET /galaxy/history command is sent. ................ - - [15/Apr/2015:13:03:43 -0700] "GET /galaxy/history HTTP/1.1" 200 - "http://salk.bccdc.med.ubc.ca/galaxy/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2272.101 Safari/537.36" ................ - - [15/Apr/2015:13:03:43 -0700] "GET /galaxy/history HTTP/1.1" 500 - "http://salk.bccdc.med.ubc.ca/galaxy/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2272.101 Safari/537.36" Error - <type 'exceptions.TypeError'>: 'NoneType' object is not callable ................ - - [15/Apr/2015:13:03:43 -0700] "GET /galaxy/root/tool_menu HTTP/1.1" 200 - "http://salk.bccdc.med.ubc.ca/galaxy/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2272.101 Safari/537.36" URL: http://salk.bccdc.med.ubc.ca/galaxy/history File '/usr/lib/python2.6/site-packages/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', line 169 in __call__ return body( environ, start_response ) File '/usr/local/galaxy/production/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 759 in render template.render_context( context ) File '/usr/local/galaxy/production/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 319 in render_context **kwargs) File '/usr/local/galaxy/production/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/local/galaxy/production/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/galaxy/production/galaxy-dist/database/compiled_templates/root/history.mako.py', line 61 in render_body __M_writer(u'\n\n') File '/usr/local/galaxy/production/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 756 in write response_write( d.encode( 'utf-8' ) ) TypeError: 'NoneType' object is not callable Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada

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Using synchronous method to upload multiple files
by Daniele P Colobraro 16 Apr '15

16 Apr '15

Hi all, I've set up a simple tool using the synchronous method to upload a file on galaxy. I'm able to visit the external link, select and upload a file by the list. The script that I use is data_source.py and the 'command' part in the xml configuration is the same as the ucsc xml config (ucsc_tablebrowser.xml). But my purpose is to import multiple files. Have you any idea how I can set a way to import/upload multiple files by using the synchronous method? Thank in advance, Best regards Daniele

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