October 2012 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Tools Always Failing?
by Nate Coraor 26 Oct '12

26 Oct '12

On Oct 25, 2012, at 4:34 PM, Yilk, Todd A wrote: > Hello all, > > I'm using a local install of Galaxy connected to a UGE cluster and Python 2.6.7. Most of my tools are reporting failures in the history with messages like: > > An error occurred running this job: (34) Job output not returned from cluster; exit status = "0" > > With the relevant lines from Galaxy's log file looking like: > > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,586 job 34 working directory is /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34 > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,636 job 34 input = [["/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat", "fastq", "5230830"]] > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,671 (34) submitting file /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/uge/galaxy_34.sh > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,672 (34) command is: memtimepro -q -o /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/34.drmmt perl /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/tools/lanl/readMapping/fastqSplitter/separate_paired_end_reads.pl -i /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat -l /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_53.dat -r /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_54.dat ; cd /opt/galaxy/dev/Galaxy-JGI_galaxy-dev; /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/set_metadata.sh ./database/files /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34 . /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/universe_wsgi.ini /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/tmp/tmp831aRx /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/galaxy.json /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_in_HistoryDatasetAssociation_59_fpBxRp,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_kwds_HistoryDatasetAssociation_59_MLg1Aw,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_out_HistoryDatasetAssociation_59_ZVYBIT,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_results_HistoryDatasetAssociation_59_q4FpIq,,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_override_HistoryDatasetAssociation_59_3HXPLq /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_in_HistoryDatasetAssociation_60_Qw0GpA,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_kwds_HistoryDatasetAssociation_60_ZF6Zk_,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_out_HistoryDatasetAssociation_60_eEItGr,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_results_HistoryDatasetAssociation_60_bMa6HN,,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_override_HistoryDatasetAssociation_60_X1El1z > galaxy.jobs.runners.drmaa INFO 2012-10-25 10:31:26,720 (34) queued as 553774 > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:28,947 (34/553774) state change: job is running > > -- snip -- > > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:32:29,411 (34/553774) state change: job finished normally > 128.165.72.57 - - [25/Oct/2012:10:32:31 -0600] "POST /root/history_item_updates HTTP/1.0" 200 - "http://galaxy-dev.lanl.gov/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:15.0) Gecko/20100101 Firefox/15.0.1" > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:32:31,241 (34) Job output not returned from cluster; exit status = "0 > " > galaxy.jobs DEBUG 2012-10-25 10:32:31,285 The tool did not define exit code or stdio handling; checking stderr for success > galaxy.jobs DEBUG 2012-10-25 10:32:31,427 setting dataset state to ERROR > galaxy.jobs DEBUG 2012-10-25 10:32:31,471 setting dataset state to ERROR > galaxy.jobs DEBUG 2012-10-25 10:32:31,728 job 34 ended > galaxy.datatypes.metadata DEBUG 2012-10-25 10:32:31,729 Cleaning up external metadata files > > > And yet, for this example, the tool did actually run successfully with the expected output files where they should be in the galaxy/database/files directory. > > Further, the 34.drmec file has just the exit code 0, the 34.drmout file is empty and the 34.drmmt file is: Hi Todd, I've moved this over to galaxy-dev since it concerns a local installation. There should be a 34.drmerr file in addition to 34.drmout and 34.drmec. If any of the three are missing or unreadable when the job finishes, you'll encounter this error. You might want to try increasing the value of "retry_job_output_collection". Also, the changes in bfbd456ebbbe will show exactly which file is causing the problem, and the error message from the OS. --nate > > { > "program": "perl", > "arguments": [ > "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/tools/lanl/readMapping/fastqSplitter/separate_paired_end_reads.pl", > "-i", > "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat", > "-l", > "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_53.dat", > "-r", > "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_54.dat" > ], > "exit_status": 0, > "start_time": 1351182686, > "wall_time": 0.223, > "usage": { > "utime": 0.04, > "stime": 0.08, > "max_vmem_kb": 11920, > "max_rss_kb": 156, > "start_time": 1351182686, > "wall_time": 0.223 > } > } > > > So everything looks good to me but Galaxy is reporting a failed run. What piece am I missing? > > Thanks! > > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

1 0

FTP upload not working
by Oliver Berkowitz 26 Oct '12

26 Oct '12

Hi, I am having an issue withuploading data via FTP. I get the following error: Response: 530 Sorry, the maximum number of clients (3) for this user are already connected. Error: Critical error Error: Could not connect to server Is this because I try to upload too many files in parallel. Should I upload only one at a time. Cheers Oliver ------------------

2 1

How are jobs controlled on a stand alone instance?
by jjv5 26 Oct '12

26 Oct '12

Hello, I cannot seem to find the details on how jobs are managed when Galaxy is run on a standalone server. Are jobs managed in a queue of some sort? Does Galaxy determine resources available in some way and moderate jobs that are run? As a specific example, we have a 40 core machine with 1TB of memory. If 10 users each submit 10 jobs each, say for a bowtie job that has been set to use 8 cores, will Galaxy sort this all out and only run jobs to fill the 40 cores? Are there settings to control this behavior without installing an external job manager like SGE? Thanks, Jim

1 0

Re: [galaxy-dev] [Patch] ToolShed support for included tools
by Greg Von Kuster 26 Oct '12

26 Oct '12

Hello Franco, These details for defining tool dependency installation for tools contained in tool shed repositories are discussed in the Galaxy tool shed wiki at http://wiki.g2.bx.psu.edu/ToolShedToolFeatures. You can also learn a lot by looking at example tool_dependency.xml files in repositories in the tool shed. These repositories in the main Galaxy tool shed provide some good examples: htseqcount, emboss_5, freebayes, picard Greg Von Kuster On Oct 26, 2012, at 1:49 AM, Franco Caramia wrote: > Hi Greg, > > Sorry to ask you something unrelated. > > Where can I find documentation about usage and syntax of tags such as : > install, package > > Is there any available? > > There has to be more than just : > http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax > > Thanks, > > Franco > > > > On 26/10/12 1:58 AM, "Greg Von Kuster" <greg(a)bx.psu.edu> wrote: > >> Hi Bjorn, >> >> I've committed an slightly altered version of your contributed code for >> handling tool dependencies that are zip archives in change set >> 8107:b12140970208, which will be available in the next Galaxy release >> currently scheduled for the end of next week. Your code required Python 2.6+, >> so I made some changes to support Python 2.5+. >> >> Please let me know if you have additional questions regarding this. >> >> Thanks very much for your contributions! >> >> Greg Von Kuster >> >> >> On Oct 15, 2012, at 1:15 PM, Björn Grüning wrote: >> >>> Hi, >>> >>> i'm writing a galaxy wrapper for bismark and trim-galore. Both are plain >>> perl scripts, that wraps around other dependencies (e.g. Bowtie). The >>> idea was to include the perl-scripts directly in the galaxy-wrapper and >>> update the PATH to the REPOSITORY_INSTALL_DIR in the tool_dependency.xml >>> file. >>> >>> ---- >>> <package name="bismark" version="0.7.7"> >>> <install version="1.0"> >>> <actions> >>> <action type="set_environment"> >>> <environment_variable name="PATH" >>> action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> >>> </action> >>> </actions> >>> </install> >>> <readme> >>> bismark, bismark_genome_preparation and bismark_methylation_extractor >>> are shipped with that wrapper >>> </readme> >>> </package> >>> ---- >>> >>> Unfortunately, that was not supported because the toolshed expected at >>> least one "action_type". The attached patch should add that feature. >>> >>> Furthermore, bowtie2 is only available as zip archive and afaik that was >>> not handled in the toolshed. The attached patch also added >>> check_zipfile(), extract_zip() and zip_extraction_directory() to fully >>> support zip archives. >>> >>> Thanks! >>> Bjoern >>> >>> <toolshed_zip.patch>_________________________________________________________ >>> __ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > > > This email (including any attachments or links) may contain > confidential and/or legally privileged information and is > intended only to be read or used by the addressee. If you > are not the intended addressee, any use, distribution, > disclosure or copying of this email is strictly > prohibited. > Confidentiality and legal privilege attached to this email > (including any attachments) are not waived or lost by > reason of its mistaken delivery to you. > If you have received this email in error, please delete it > and notify us immediately by telephone or email. Peter > MacCallum Cancer Centre provides no guarantee that this > transmission is free of virus or that it has not been > intercepted or altered and will not be liable for any delay > in its receipt. > >

1 0

Tools Always Failing?
by Jennifer Jackson 25 Oct '12

25 Oct '12

Re-post to galaxy-dev(a)bx.psu.edu Todd - this will give your questions better visibility. This is your own tool? And other tools packaged with the standard Galaxy distribution or installed from the Tool Shed run OK on the cluster? If your own tool (and others work, ruling out cluster set-up as an issue), you are probably already working from this wiki, but if not, section #42 covers exit codes: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax Let's see what other feedback/advice comes from the developers, Best, Jen Galaxy team On 10/25/12 1:34 PM, Yilk, Todd A wrote: > Hello all, > > I'm using a local install of Galaxy connected to a UGE cluster and > Python 2.6.7. Most of my tools are reporting failures in the history > with messages like: > > An error occurred running this job: /(34) Job output not returned > from cluster; exit status = "0"/ > / > / > With the relevant lines from Galaxy's log file looking like: > > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,586 job 34 working > directory is > /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34 > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,636 job 34 input = > [["/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat", > "fastq", "5230830"]] > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,671 (34) > submitting file > /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/uge/galaxy_34.sh > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,672 (34) command > is: memtimepro -q -o > /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/34.drmmt > perl > /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/tools/lanl/readMapping/fastqSplitter/separate_paired_end_reads.pl > -i > /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat > -l > /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_53.dat > -r > /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_54.dat ; > cd /opt/galaxy/dev/Galaxy-JGI_galaxy-dev; > /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/set_metadata.sh ./database/files > /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34 > . /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/universe_wsgi.ini > /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/tmp/tmp831aRx > /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/galaxy.json > /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_in_HistoryDatasetAssociation_59_fpBxRp,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_kwds_HistoryDatasetAssociation_59_MLg1Aw,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_out_HistoryDatasetAssociation_59_ZVYBIT,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_results_HistoryDatasetAssociation_59_q4FpIq,,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_override_HistoryDatasetAssociation_59_3HXPLq > /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_in_HistoryDatasetAssociation_60_Qw0GpA,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_kwds_HistoryDatasetAssociation_60_ZF6Zk_,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_out_HistoryDatasetAssociation_60_eEItGr,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_results_HistoryDatasetAssociation_60_bMa6HN,,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_override_HistoryDatasetAssociation_60_X1El1z > galaxy.jobs.runners.drmaa INFO 2012-10-25 10:31:26,720 (34) queued as > 553774 > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:28,947 (34/553774) > state change: job is running > > -- snip -- > > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:32:29,411 (34/553774) > state change: job finished normally > 128.165.72.57 - - [25/Oct/2012:10:32:31 -0600] "POST > /root/history_item_updates HTTP/1.0" 200 - > "http://galaxy-dev.lanl.gov/history" "Mozilla/5.0 (Macintosh; Intel > Mac OS X 10.6; rv:15.0) Gecko/20100101 Firefox/15.0.1" > galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:32:31,241 (34) Job > output not returned from cluster; exit status = "0 > " > galaxy.jobs DEBUG 2012-10-25 10:32:31,285 The tool did not define exit > code or stdio handling; checking stderr for success > galaxy.jobs DEBUG 2012-10-25 10:32:31,427 setting dataset state to ERROR > galaxy.jobs DEBUG 2012-10-25 10:32:31,471 setting dataset state to ERROR > galaxy.jobs DEBUG 2012-10-25 10:32:31,728 job 34 ended > galaxy.datatypes.metadata DEBUG 2012-10-25 10:32:31,729 Cleaning up > external metadata files > > > And yet, for this example, the tool did actually run successfully with > the expected output files where they should be in the > galaxy/database/files directory. > > Further, the 34.drmec file has just the exit code 0, the 34.drmout > file is empty and the 34.drmmt file is: > > { > "program": "perl", > "arguments": [ > "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/tools/lanl/readMapping/fastqSplitter/separate_paired_end_reads.pl", > "-i", > "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat", > "-l", > "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_53.dat", > "-r", > "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_54.dat" > ], > "exit_status": 0, > "start_time": 1351182686, > "wall_time": 0.223, > "usage": { > "utime": 0.04, > "stime": 0.08, > "max_vmem_kb": 11920, > "max_rss_kb": 156, > "start_time": 1351182686, > "wall_time": 0.223 > } > } > > > So everything looks good to me but Galaxy is reporting a failed run. > What piece am I missing? > > Thanks! > > > > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org

1 0

[Patch] ToolShed support for included tools
by Björn Grüning 25 Oct '12

25 Oct '12

Hi, i'm writing a galaxy wrapper for bismark and trim-galore. Both are plain perl scripts, that wraps around other dependencies (e.g. Bowtie). The idea was to include the perl-scripts directly in the galaxy-wrapper and update the PATH to the REPOSITORY_INSTALL_DIR in the tool_dependency.xml file. ---- <package name="bismark" version="0.7.7"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> bismark, bismark_genome_preparation and bismark_methylation_extractor are shipped with that wrapper </readme> </package> ---- Unfortunately, that was not supported because the toolshed expected at least one "action_type". The attached patch should add that feature. Furthermore, bowtie2 is only available as zip archive and afaik that was not handled in the toolshed. The attached patch also added check_zipfile(), extract_zip() and zip_extraction_directory() to fully support zip archives. Thanks! Bjoern

2 2

Error when creating Visualization
by Andreas Kuntzagk 25 Oct '12

25 Oct '12

Hi, on our local Galaxy instance I try to setup Visualization. I followed http://wiki.g2.bx.psu.edu/Learn/Visualization#Setup_for_Local_Instances But when I try to create a new visalization I get an error with this traceback: URL: http://bbc.mdc-berlin.de/galaxy/visualization/create File '/data/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/data/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/data/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/data/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/data/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/data/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 93 in decorator return func( self, trans, *args, **kwargs ) File '/data/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/visualization.py', line 590 in create type=visualization_type ) File '/data/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py', line 343 in create_visualization revision = trans.model.VisualizationRevision( visualization=visualization, title=title, config=config, dbkey=dbkey ) File '<string>', line 4 in __init__ File '/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/state.py', line 82 in initialize_instance return manager.events.original_init(*mixed[1:], **kwargs) File '/data/galaxy/galaxy-dist/lib/galaxy/model/__init__.py', line 2764 in __init__ self.visualization = visualization File '/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py', line 150 in __set__ self.impl.set(instance_state(instance), instance_dict(instance), value, None) File '/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py', line 590 in set value = self.fire_replace_event(state, dict_, value, old, initiator) File '/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py', line 610 in fire_replace_event value = ext.set(state, value, previous, initiator or self) File '/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py', line 847 in set new_state, new_dict = instance_state(child), instance_dict(child) AttributeError: 'dict' object has no attribute '_sa_instance_state' Any idea what may be wrong? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

1 1

the multi job splitter
by Jorrit Boekel 25 Oct '12

25 Oct '12

Dear list, In my galaxy fork, I extensively use the job splitters. Sometimes though, I have to split to different file types for the same job. That raises an exception in the lib/galaxy/jobs/splitters/multi.py module. I have turned this behaviour off for my own work, but am now wondering whether this is very bad practice. In other words, does somebody know why the multi splitter does not support multiple file type splitting? cheers, jorrit -- Scientific programmer Mass spec analysis support @ BILS Janne Lehtiö / Lukas Käll labs SciLifeLab Stockholm

2 6

Data library displays "(OperationError) no such column" error
by Xinyi Chua 24 Oct '12

24 Oct '12

Hi all, After updating my galaxy-dist to the latest release (23/Oct) I get the following error message when I try to access one of my data libraries. Error attempting to display contents of library (testlibrary): (OperationalError) no such column: True u'SELECT dataset_permissions.id AS dataset_permissions_id, dataset_permissions.create_time AS dataset_permissions_create_time, dataset_permissions.update_time AS dataset_permissions_update_time, dataset_permissions.action AS dataset_permissions_action, dataset_permissions.dataset_id AS dataset_permissions_dataset_id, dataset_permissions.role_id AS dataset_permissions_role_id XnFROM dataset_permissions XnWHERE True AND dataset_permissions.action = ?' ['access']. I was getting the same error message as the previous post (http://gmod.827538.n3.nabble.com/quot-No-module-named-controllers-library-c…) before the update and it’s now replaced with the above. I’ve also tried cloning a fresh galaxy-dist but I’m still receiving the same error message. The library exists and files are present because I can see them when I go to http://localhost:8080/api/libraries/XXXXX ... I just cannot access it via the web interface. Has anyone experienced a similar situation, or have any ideas? Many Thanks, Xin-Yi

1 0

Importing files into Libraries
by Neil.Burdett＠csiro.au 24 Oct '12

24 Oct '12

Hi, If we upload data and then import the data into libraries, how is that data then accessed when running a tool in the cloud. For example if we have hundreds of template files that we need to analyse the data, and we have a tool that is instantiated on a number of nodes in the clous, is the data in the libraries copied to each node? Or is the data access via nfs, symbolic link or some other method? Thanks Neil

2 2