May 2010 - galaxy-dev - lists.galaxyproject.org

python segfaults
by Chris Zaleski 20 May '10

20 May '10

Greetings, I'm unfortunately having problems with segfaults on my server. The server runs CentOS, with python version 2.4.3. After installing & setting up Galaxy, there have been an increasing number of segfaults thrown by multiple processes. Originally there were 2 distinct tools (which were run by Galaxy) that had thrown segfaults, *and* Galaxy's own python process was throwing segfaults as well. This is happening with increasing frequency. Most recently python is throwing the segfault (and galaxy dies) before we can even run any tools. Syslog eg: May 18 13:29:12 florence kernel: python[10657]: segfault at 00002aab33ff1000 rip 00000033a427bf0b rsp 000000004942ac38 error 6 Notes: 1) We ran a full spectrum of hardware diagnostics which found no problems. 2) This morning while in the process of troubleshooting, I rebooted the server. Galaxy started as a service, and *threw another segfault shortly after instantiating* - long before anyone could have interacted with the server. This leads me to believe the problem is python related. I plan to upgrade python, possibly go through some core dumps, etc. However before going any further, I wanted to see if any had experience with a similar problem. Any information is appreciated. Thanks very much, Chris Zaleski CSHL

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Metadata indexing slow on large files
by Dennis Gascoigne 20 May '10

20 May '10

We are working with some very large sequence libraries (paired end 70M reads+ each end - 15Gbx2). We already know what the file types are and that they are appropriate for the pipeline. There seems to be a large amount of the processing effort expended after the completion after each step in the workflow analysing the files and determining their attributes - this is related to the size of the files (which are large at every step) and is of no practical use to us, except maybe on the final step. Is there any way to suppress post processing steps and simply accept the file as specified in the tool output tags? How can we reduce or eliminate verification/indexing on metadata tags - what implications should we be aware of. Thanks dennis

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proper setup of postgres
by Davide Cittaro 20 May '10

20 May '10

Hi there, I'm trying to setup postgres for galaxy, and this should be easy... nevertheless I get authentication errors as I start galaxy. I'm not a postgres expert, but this line local all all ident sameuser in pg_hba.conf should enable access to local users but then: $ ./run.sh […] galaxy.model.migrate.check DEBUG 2010-05-20 14:11:02,248 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/data/galaxy_dist/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/data/galaxy_dist/lib/galaxy/app.py", line 28, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/data/galaxy_dist/lib/galaxy/model/migrate/check.py", line 54, in create_or_verify_database dataset_table = Table( "dataset", meta, autoload=True ) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py", line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py", line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1261, in reflecttable conn = self.contextual_connect() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/threadlocal.py", line 194, in contextual_connect return self.session.get_connection(**kwargs) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/threadlocal.py", line 20, in get_connection return self.engine.TLConnection(self, self.engine.pool.connect(), close_with_result=close_with_result) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 151, in connect agent = _ConnectionFairy(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 304, in __init__ rec = self._connection_record = pool.get() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 161, in get return self.do_get() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 639, in do_get con = self.create_connection() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 122, in create_connection return _ConnectionRecord(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 198, in __init__ self.connection = self.__connect() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/pool.py", line 261, in __connect connection = self.__pool._creator() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/strategies.py", line 80, in connect raise exc.DBAPIError.instance(None, None, e) OperationalError: (OperationalError) FATAL: Ident authentication failed for user "galaxy" None None This is true for root also. Any hint appreciated :-) d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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Problem in bx-python 0.5 maf functions
by Dennis Gascoigne 19 May '10

19 May '10

There is a problem with the 0.5 bx-python build used in Galaxy (that i think has been fixed in 0.6) can you please update the central repository to include 0.6 ASAP please? Basically, if you try to run maf join (or other functions maf tools) and select a genome that is not present in the first block, you will get an empty file returned. It seems from the descriptions on James' site that this may be fixed in 0.6 -- Dennis Gascoigne

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Conditional tag error
by Modi, Amit 19 May '10

19 May '10

Hi, I am trying to use conditional tag as per the instructions specified. This is the code I wrote in xml file I created for my tool: <tool id="gKelvinTest" name="GKelvin Step"> <description>Test conditions for gKelvin.</description> <command> #if $test.confile=="metadata": #gkelvin $test.meta #else: #gkelvin $test.nonmeta #end </command> <inputs> <conditional name="test"> <param name="confile" type="data" label="Configuration File"> <option value="metadata">With Metadata</option> <option value="no_metadata">Without Metadata</option> </param> <when value="metadata"> <param name="meta" type="select" label="Metadata info"> <option value="0">0</option> <option value="1">1</option> <option value="2">2</option> <option value="3">3</option> <option value="4">4</option> <option value="5">5</option> </param> </when> <when value="no_metadata"> <param name="nonmeta" type="text" label="No metadata Info" /> </when> </conditional> </inputs> <help> Will Run Kelvin. </help> </tool> But I get the following error. Error Traceback: View as: Interactive | Text | XML (full) ⇝ Exception: ('No case matched value:', 'test', <galaxy.model.HistoryDatasetAssociation object at 0x214c6ed0>) URL: http://10.70.250.254:8080/tool_runner?tool_id=gKelvinTest Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:97 in __call__ view >> status, headers, body = wsgilib.intercept_output( Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:125 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.controllers.tool_runner:53 in index view >> template, vars = tool.handle_input( trans, params.__dict__ ) Module galaxy.tools:759 in handle_input view >> state = self.new_state( trans ) Module galaxy.tools:681 in new_state view >> self.fill_in_new_state( trans, inputs, state.inputs ) Module galaxy.tools:691 in fill_in_new_state view >> state[ input.name ] = input.get_initial_value( trans, context ) Module galaxy.tools.parameters.grouping:408 in get_initial_value view >> current_case = self.get_current_case( test_value, trans ) Module galaxy.tools.parameters.grouping:365 in get_current_case view >> raise Exception( "No case matched value:", self.name, str_value ) Exception: ('No case matched value:', 'test', <galaxy.model.HistoryDatasetAssociation object at 0x214c6ed0>) Extra Features >> Display the lines of code near each part of the traceback Show a debug prompt to allow you to directly debug the code at the traceback Re-GET Page Any help would be appreciated, Thanks a lot Regards, Amit Modi ----------------------------------------- Confidentiality Notice: The following mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. The recipient is responsible to maintain the confidentiality of this information and to use the information only for authorized purposes. If you are not the intended recipient (or authorized to receive information for the intended recipient), you are hereby notified that any review, use, disclosure, distribution, copying, printing, or action taken in reliance on the contents of this e-mail is strictly prohibited. If you have received this communication in error, please notify us immediately by reply e-mail and destroy all copies of the original message. Thank you.

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Galaxy on the cloud problem
by Martin Paradesi 19 May '10

19 May '10

Hello Galaxy team, I tried to setup Galaxy on the cloud with my Amazon Web Services account but I'm getting the following message: "The Galaxy Cloud Console is not running. It may take a few moments to start after your EC2 instance has become available, or you may not have provided the correct user data when configuring and launching the instance from the AWS Management Console. Please refer to the documentation for more information. If you did enter the correct user data, you may be able to reboot this EC2 instance to solve the problem." even after running the instance for an hour. I'm using AMI ID: ami-ed03ed84 and have set appropriate security groups, key pair and user data. I have also rebooted the instance few times. I have attached a snapshot of the server log for your perusal. init: console-setup main process (79) terminated with status 1 %Ginit: plymouth main process (61) killed by SEGV signal init: plymouth-splash main process (238) terminated with status 2 Generating locales... en_US.UTF-8... up-to-date Generation complete. mountall: Disconnected from Plymouth mountall: Skipping mounting /mnt since Plymouth is not available init: plymouth-log main process (392) terminated with status 1 Generating public/private rsa key pair. Your identification has been saved in /etc/ssh/ssh_host_rsa_key. Your public key has been saved in /etc/ssh/ssh_host_rsa_key.pub. The key fingerprint is: <snip></snip> The key's randomart image is: Generating public/private dsa key pair. Your identification has been saved in /etc/ssh/ssh_host_dsa_key. Your public key has been saved in /etc/ssh/ssh_host_dsa_key.pub. The key fingerprint is: <snip></snip> The key's randomart image is: ec2: ec2: ############################################################# ec2: -----BEGIN SSH HOST KEY FINGERPRINTS----- ec2: -----END SSH HOST KEY FINGERPRINTS----- ec2: ############################################################# * Starting AppArmor profiles [80G [74G[ OK ] * Exporting directories for NFS kernel daemon... [80G exportfs: Warning: /mnt/galaxyTools does not exist exportfs: Warning: /mnt/galaxyIndices does not exist exportfs: Warning: /mnt/galaxyData does not exist [74G[ OK ] * Starting NFS kernel daemon [80G [74G[ OK ] Starting PostgreSQL 8.4: waiting for server to start...sh: cannot create /mnt/galaxyData/pgsql/data/pg_log/startup.log: Directory nonexistent ............................................................could not start server PostgreSQL 8.4 did not start in a timely fashion, please see /mnt/galaxyData/pgsql/data/pg_log/startup.log for details Starting rabbitmq-server: SUCCESS rabbitmq-server. landscape-client is not configured, please run landscape-config. Unzipping file ec2autorun.zip Ubuntu lucid (development branch) ip-10-245-189-171 tty1 ip-10-245-189-171 login: Can you please let me know what could be going wrong? Thanks, Martin

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Galaxy on the cloud problem
by Michael Pheasant 18 May '10

18 May '10

We have the exact same problem. Any ideas? Cheers, Mike. -- Michael Pheasant Software Engineer Queensland Facility for Advanced Bioinformatics Level 6, QBP University of Queensland, QLD 4072 T: +61 (0)7 3346 2070 F: +61 (0)7 3346 2101 www.qfab.org

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Add genome for bowtie
by padioleau 17 May '10

17 May '10

Dear galaxy developers, I'm curently working on my local galaxy and I encountered some difficulties to add new genomes. I'm working with the "bowtie mapping" and "sam_to_bam tools" and the problem was that my galaxy was not able to automatically set the genome of the output in my history. I was forced to change it by hand before I could launch "sam_to_bam" on my data. For this reason, my workflow including these two steps would fail. I finally figure out the problem: my dbkey (i.e: reference in build.txt) for my genome wasn't identical to the name of my ebwt file (i.e: my local indexe files for bowtie). Changing the name so that they are identical (case sensitive!) solved the problem. This wasn't mentioned anywhere, neither in the bowtie_indices.loc.sample file, not in the builds.txt.sample one. I've spent a couple of hour to figure out what the problem was. It would be great if you could write something about that in both files or at least in bowtie_indices.loc.sample Ismael -- Padioleau Ismael EMBL Heidelberg ( V205)

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Metadata for large fastq files is slow...
by Dennis Gascoigne 17 May '10

17 May '10

We are working with some very large sequence libraries (paired end 70M reads+ each end - 15Gbx2). We already know what the file types are and that they are appropriate for the pipeline. There seems to be a large amount of the processing effort expended after the completion after each step in the workflow analysing the files and determining their attributes - this is related to the size of the files (which are large at every step) and is of no practical use to us, except maybe on the final step. Is there any way to suppress post processing steps and simply accept the file as specified in the tool output tags? How can we reduce or eliminate verification/indexing on metadata tags - what implications should we be aware of. -- Dennis Gascoigne 0407 639 995 dennis.gascoigne(a)gmail.com

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Error in file upload for new metadata
by Modi, Amit 14 May '10

14 May '10

Hi, I created a metadata to hold 5 files together (1 primary and 4 data files). The file extension corresponding to the following metadata appears correctly in the list. But When I try to upload the files. I get the following error. Could you please help me fix this. Here is the small class that I created to hold metadata: class CompositeTest( Data ): file_ext="comptest" MetadataElement( name="data_lines", default=0, desc="Number of data lines", readonly=True, optional=True, visible=False, no_value=0 ) composite_type="basic" def __init__(self,**kwd): Data.__init__(self,**kwd) self.add_composite_file('pedfile.txt') self.add_composite_file('mapfile.txt') self.add_composite_file('frequencyfile.txt') self.add_composite_file('datafile.txt') def init_meta(self,dataset,copy_from=None ): Data.init_meta(self,dataset,copy_from=copy_from) Source Template Extra Data Traceback Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'Bunch' object has no attribute 'space_to_tab' URL: http://10.70.250.254:8080/tool_runner/index Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:97 in __call__ view >> status, headers, body = wsgilib.intercept_output( Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:125 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.controllers.tool_runner:53 in index view >> template, vars = tool.handle_input( trans, params.__dict__ ) Module galaxy.tools:795 in handle_input view >> _, out_data = self.execute( trans, incoming=params ) Module galaxy.tools:1067 in execute view >> return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) Module galaxy.tools.actions.upload:18 in execute view >> uploaded_datasets = upload_common.get_uploaded_datasets( trans, incoming, precreated_datasets, dataset_upload_inputs ) Module galaxy.tools.actions.upload_common:214 in get_uploaded_datasets view >> uploaded_datasets.extend( dataset_upload_input.get_uploaded_datasets( trans, params ) ) Module galaxy.tools.parameters.grouping:301 in get_uploaded_datasets view >> dataset.space_to_tab = file_bunch.space_to_tab AttributeError: 'Bunch' object has no attribute 'space_to_tab' Extra Features >> Display the lines of code near each part of the traceback Show a debug prompt to allow you to directly debug the code at the traceback In Text Tab : URL: http://10.70.250.254:8080/tool_runner/index File '/export/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.4.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/debug/prints.py', line 97 in __call__ status, headers, body = wsgilib.intercept_output( File '/export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/export/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/export/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/tool_runner.py', line 53 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 795 in handle_input _, out_data = self.execute( trans, incoming=params ) File '/export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 1067 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) File '/export/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/upload.py', line 18 in execute uploaded_datasets = upload_common.get_uploaded_datasets( trans, incoming, precreated_datasets, dataset_upload_inputs ) File '/export/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/upload_common.py', line 214 in get_uploaded_datasets uploaded_datasets.extend( dataset_upload_input.get_uploaded_datasets( trans, params ) ) File '/export/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py', line 301 in get_uploaded_datasets dataset.space_to_tab = file_bunch.space_to_tab AttributeError: 'Bunch' object has no attribute 'space_to_tab' In XML(full) TAB: <?xml version="1.0" ?> <traceback> <sysinfo> <language version="2.4.3"> Python </language> </sysinfo> <stack> <frame> <module> weberror.evalexception.middleware </module> <filename> /export/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.4.egg/weberror/evalexception/middleware.py </filename> <line> 364 </line> <function> respond </function> <operation> app_iter = self.application(environ, detect_start_response) </operation> <operation_context> try: __traceback_supplement__ = errormiddleware.Supplement, self, environ app_iter = self.application(environ, detect_start_response) try: return_iter = list(app_iter) </operation_context> </frame> <frame> <module> paste.debug.prints </module> <filename> /export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/debug/prints.py </filename> <line> 97 </line> <function> __call__ </function> <operation> status, headers, body = wsgilib.intercept_output( </operation> <operation_context> threadedprint.register(replacement_stdout) try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: </operation_context> </frame> <frame> <module> paste.wsgilib </module> <filename> /export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/wsgilib.py </filename> <line> 539 </line> <function> intercept_output </function> <operation> app_iter = application(environ, replacement_start_response) </operation> <operation_context> data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter) </operation_context> </frame> <frame> <module> paste.recursive </module> <filename> /export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/recursive.py </filename> <line> 80 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware( </operation_context> </frame> <frame> <module> paste.httpexceptions </module> <filename> /export/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.4.egg/paste/httpexceptions.py </filename> <line> 632 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response) </operation_context> </frame> <frame> <module> galaxy.web.framework.base </module> <filename> /export/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py </filename> <line> 125 </line> <function> __call__ </function> <operation> body = method( trans, **kwargs ) </operation> <operation_context> kwargs.pop( '_', None ) try: body = method( trans, **kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs ) </operation_context> </frame> <frame> <module> galaxy.web.controllers.tool_runner </module> <filename> /export/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/tool_runner.py </filename> <line> 53 </line> <function> index </function> <operation> template, vars = tool.handle_input( trans, params.__dict__ ) </operation> <operation_context> # so make sure to create a new history if we've never had one before. history = trans.get_history( create=True ) template, vars = tool.handle_input( trans, params.__dict__ ) if len(params) > 0: trans.log_event( "Tool params: %s" % (str(params)), tool_id=tool_id ) </operation_context> </frame> <frame> <module> galaxy.tools </module> <filename> /export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py </filename> <line> 795 </line> <function> handle_input </function> <operation> _, out_data = self.execute( trans, incoming=params ) </operation> <operation_context> # If we've completed the last page we can execute the tool elif state.page == self.last_page: _, out_data = self.execute( trans, incoming=params ) try: assert isinstance( out_data, odict ) </operation_context> </frame> <frame> <module> galaxy.tools </module> <filename> /export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py </filename> <line> 1067 </line> <function> execute </function> <operation> return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) </operation> <operation_context> when run will build the tool's outputs, e.g. `DefaultToolAction`. """ return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) def params_to_strings( self, params, app ): </operation_context> </frame> <frame> <module> galaxy.tools.actions.upload </module> <filename> /export/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/upload.py </filename> <line> 18 </line> <function> execute </function> <operation> uploaded_datasets = upload_common.get_uploaded_datasets( trans, incoming, precreated_datasets, dataset_upload_inputs ) </operation> <operation_context> precreated_datasets = upload_common.get_precreated_datasets( trans, incoming, trans.app.model.HistoryDatasetAssociation ) incoming = upload_common.persist_uploads( incoming ) uploaded_datasets = upload_common.get_uploaded_datasets( trans, incoming, precreated_datasets, dataset_upload_inputs ) upload_common.cleanup_unused_precreated_datasets( precreated_datasets ) </operation_context> </frame> <frame> <module> galaxy.tools.actions.upload_common </module> <filename> /export/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/upload_common.py </filename> <line> 214 </line> <function> get_uploaded_datasets </function> <operation> uploaded_datasets.extend( dataset_upload_input.get_uploaded_datasets( trans, params ) ) </operation> <operation_context> uploaded_datasets = [] for dataset_upload_input in dataset_upload_inputs: uploaded_datasets.extend( dataset_upload_input.get_uploaded_datasets( trans, params ) ) for uploaded_dataset in uploaded_datasets: data = get_precreated_dataset( precreated_datasets, uploaded_dataset.name ) </operation_context> </frame> <frame> <module> galaxy.tools.parameters.grouping </module> <filename> /export/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py </filename> <line> 301 </line> <function> get_uploaded_datasets </function> <operation> dataset.space_to_tab = file_bunch.space_to_tab </operation> <operation_context> writable_files_offset = 1 dataset.primary_file = file_bunch.path dataset.space_to_tab = file_bunch.space_to_tab dataset.precreated_name = file_bunch.precreated_name dataset.name = file_bunch.precreated_name </operation_context> </frame> </stack> <exception> <type> AttributeError </type> <value> 'Bunch' object has no attribute 'space_to_tab' </value> </exception> </traceback> Thanks and Regards, Amit Modi ----------------------------------------- Confidentiality Notice: The following mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. The recipient is responsible to maintain the confidentiality of this information and to use the information only for authorized purposes. If you are not the intended recipient (or authorized to receive information for the intended recipient), you are hereby notified that any review, use, disclosure, distribution, copying, printing, or action taken in reliance on the contents of this e-mail is strictly prohibited. If you have received this communication in error, please notify us immediately by reply e-mail and destroy all copies of the original message. Thank you.

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