- galaxy-dev - lists.galaxyproject.org

Metadata recursion error with empty tabular file (with patch)
by Peter Cock 18 Mar '11

18 Mar '11

Hi all, I just got a nasty recursion error when trying to run the functional tests for my TMHMM and SignalP wrappers - tools which produce tabular output. galaxy.jobs.runners.local: ERROR: Job wrapper finish method failed Traceback (most recent call last): File "/home/pjcock/repositories/galaxy-central/lib/galaxy/jobs/runners/local.py", line 125, in run_job job_wrapper.finish( stdout, stderr ) File "/home/pjcock/repositories/galaxy-central/lib/galaxy/jobs/__init__.py", line 578, in finish dataset.set_peek() File "/home/pjcock/repositories/galaxy-central/lib/galaxy/model/__init__.py", line 690, in set_peek return self.datatype.set_peek( self, is_multi_byte=is_multi_byte ) File "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/tabular.py", line 227, in set_peek data.Text.set_peek( self, dataset, line_count=line_count, is_multi_byte=is_multi_byte ) File "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/data.py", line 431, in set_peek self.set_peek(dataset) ... File "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/tabular.py", line 227, in set_peek data.Text.set_peek( self, dataset, line_count=line_count, is_multi_byte=is_multi_byte ) File "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/data.py", line 431, in set_peek self.set_peek(dataset) ... File "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/tabular.py", line 227, in set_peek data.Text.set_peek( self, dataset, line_count=line_count, is_multi_byte=is_multi_byte ) File "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/data.py", line 419, in set_peek dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) File "/home/pjcock/repositories/galaxy-central/lib/galaxy/model/__init__.py", line 628, in get_file_name return self.dataset.get_file_name() File "/home/pjcock/repositories/galaxy-central/lib/galaxy/model/__init__.py", line 515, in get_file_name return os.path.abspath( os.path.join( dir, "dataset_%d.dat" % self.id ) ) File "/usr/local/lib/python2.6/posixpath.py", line 348, in abspath return normpath(path) File "/usr/local/lib/python2.6/posixpath.py", line 314, in normpath slash, dot = (u'/', u'.') if isinstance(path, unicode) else ('/', '.') RuntimeError: maximum recursion depth exceeded while calling a Python object >From the trace, two set_peek methods are calling each other in a loop. I deduced the problem was an empty tabular files, where dataset.metadata.data_lines is zero, but the test should really have been for None. Please review and apply this patch which appears to correctly resolve the issue: diff -r 9fae539215be lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Fri Mar 18 11:46:48 2011 +0000 +++ b/lib/galaxy/datatypes/data.py Fri Mar 18 11:49:05 2011 +0000 @@ -422,7 +422,7 @@ dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) if line_count is None: # See if line_count is stored in the metadata - if dataset.metadata.data_lines: + if dataset.metadata.data_lines is not None: dataset.blurb = "%s %s" % ( util.commaify( str(dataset.metadata.data_lines) ), inflector.cond_plural(dataset.metadata.data_lines, "line") ) else: # Number of lines is not known ( this should not happen ), and auto-detect is Thanks, Peter

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History information popup broken on library entries?
by Peter Cock 18 Mar '11

18 Mar '11

Hi all, I've been exploring how to use Galaxy's shared library functionality, and have noticed that once imported into a working history, that the little 'i' information icon's black popup window isn't working for these datasets. All it says is 'Could not find the job for this dataset.' This appears to affect multiple file types (FASTA and BAM tested) and both files copied into Galaxy or linked to at import. I'm using the current latest code from galaxy-central, https://bitbucket.org/galaxy/galaxy-central/changeset/e39495db6071 This also seems to affect http://test.g2.bx.psu.edu/ and also http://main.g2.bx.psu.edu/ Can anyone confirm this behaviour? I'm using Firefox on the Mac, but I doubt that is relevant. Peter

2 1

cufflinks libz error/warning
by Ryan Golhar 18 Mar '11

18 Mar '11

Hi all - I'm running Galaxy on my Redhat linux cluster. When I run cufflinks from the shell I get the error/warning: cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks) but it still seems to run ok. It looks like Galaxy is choking on this. I tried compling cufflinks manually but that was more troublesome. Is there a way I can get Galaxy to ignore this error and continue? -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

3 6

Re: [galaxy-dev] Display of tabular data in Galaxy
by Leighton Pritchard 18 Mar '11

18 Mar '11

Hi, On Mon, Oct 18, 2010 at 3:50 PM, Peter <[hidden email] <http://gmod.827538.n3.nabble.com/user/SendEmail.jtp?type=node&node=1944865& i=0&by-user=t> > wrote: > On Mon, Oct 18, 2010 at 3:28 PM, Hans-Rudolf Hotz <[hidden email] <http://gmod.827538.n3.nabble.com/user/SendEmail.jtp?type=node&node=1944865&… by-user=t> > wrote: >> On 10/18/2010 01:02 PM, Peter wrote: >>> However, on the main central column, when viewing a tabular dataset >>> (by clicking on the eye icon from an entry in the right hand column), >>> the data is shown as raw text. [...] >>> It would be nice if the main display showed the data respecting the >>> columns. Has this been considered? My guess is that doing this was >>> rejected due to the computational load to reformat it, and the network >>> load to send the marked up data. >>> >> Actually, I prefer the raw text. > > OK, but is that a typical view from the average Galaxy end user? Many > biologists I know *like* their Excel spreadsheets, and would probably > be more comfortable to see their columns of data lined up (rather than > the mess you can get with raw tab separated text). FWIW, I would prefer to see tabular display, particularly when working with (over the shoulder of...) biologists - it makes it much easier to follow the data and is, as Peter says, more in line with what they expect. There are occasions (cut-and-paste, mostly) where raw text is better, for me. Is there perhaps a possible compromise where the user can select between raw text and tabular display? L. -- Dr Leighton Pritchard MRSC Plant Pathology Programme, SCRI (C block) Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA e:lpritc@scri.ac.uk w:http://www.scri.ac.uk/staff/leightonpritchard gpg/pgp: 0xFEFC205C tel: No telephone during office refurbishment [The James Hutton Institute logo] Please note that from 1 April 2011, SCRI and the Macaulay Land Use Research Institute will join to become The James Hutton Institute. ______________________________________________________ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster(a)scri.ac.uk quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). ______________________________________________________

1 0

Problem upgrading DB from 73 to 75 (on SQLite)
by Peter Cock 18 Mar '11

18 Mar '11

Hi all, I've just updated my Mac development machine with the latest galaxy-central, and run.sh tells me the database needs to be updated from 73 to 75. Note this is running on SQLite. Running manage_db.sh upgrade gives an ImportError: No module named migrate.versioning.shell I just grabbed a fresh hg clone and it worked, but in case there is an obvious bug lurking here, the full output is below (and I'll keep the broken install on disk a bit longer in case there is anything else you need to know). Regards, Peter -- $ ./run.sh python path is: /Users/pjcock/repositories/galaxy-central/eggs/numpy-1.3.0-py2.5-macosx-10.3-fat-ucs2.egg, /Users/pjcock/repositories/galaxy-central/eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.5-macosx-10.3-fat-ucs2.egg, /Users/pjcock/repositories/galaxy-central/eggs/Whoosh-0.3.18-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/pycrypto-2.0.1-py2.5-macosx-10.3-fat-ucs2.egg, /Users/pjcock/repositories/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.5-macosx-10.3-fat-ucs2.egg, /Users/pjcock/repositories/galaxy-central/eggs/bx_python-0.7.0_14b6a6c95da6-py2.5-macosx-10.3-fat-ucs2.egg, /Users/pjcock/repositories/galaxy-central/eggs/amqplib-0.6.1-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/pexpect-2.4-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/Babel-0.9.4-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/Beaker-1.4-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/Mako-0.2.5-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/WebHelpers-0.2-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/simplejson-2.1.1-py2.5-macosx-10.3-fat-ucs2.egg, /Users/pjcock/repositories/galaxy-central/eggs/wchartype-0.1-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/docutils-0.7-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/WebOb-0.8.5-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/Routes-1.12.3-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/Cheetah-2.2.2-py2.5-macosx-10.3-fat-ucs2.egg, /Users/pjcock/repositories/galaxy-central/eggs/PasteDeploy-1.3.3-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/PasteScript-1.7.3-py2.5.egg, /Users/pjcock/repositories/galaxy-central/eggs/Paste-1.6-py2.5.egg, /Users/pjcock/repositories/galaxy-central/lib, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/setuptools-0.6c8-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/MySQL_python-1.2.2-py2.5-macosx-10.3-i386.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/TurboGears-1.0.7-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/TurboKid-1.0.4-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/TurboJson-1.1.4-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/TurboCheetah-1.0-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/RuleDispatch-0.5a0.dev_r2306-py2.5-macosx-10.5-i386.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/FormEncode-1.1-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/DecoratorTools-1.7-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/configobj-4.5.3-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/CherryPy-2.3.0-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/kid-0.9.6-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/PyProtocols-1.0a0dev_r2302-py2.5-macosx-10.3-i386.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Genshi-0.5.1-py2.5-macosx-10.3-i386.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pydot-1.0.2-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/logilab_common-0.48.0-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/logilab_astng-0.19.3-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pylint-0.19.0-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/nose-0.11.3-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/buildbot_slave-0.8.2-py2.5.egg, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib-1.0.1_r0-py2.6-macosx-10.3-fat.egg, /usr/local/lib/wxPython-unicode-2.8.10.1/lib/python2.5/site-packages, /usr/local/lib/wxPython-unicode-2.8.10.1/lib/python2.5/site-packages/wx-2.8-mac-unicode, /Library/Frameworks/Python.framework/Versions/2.5/lib/python25.zip, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-darwin, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat-mac/lib-scriptpackages, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-tk, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Numeric, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/PIL, /usr/local/lib/wxPython-unicode-2.8.10.1/lib/python2.5, /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,494 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,499 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,504 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,505 Loaded display application 'genetrack_interval' for datatype 'bed', inherit=False galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,509 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,513 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,526 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,527 Loaded display application 'genetrack_interval' for datatype 'interval', inherit=True galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,537 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,542 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,546 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False galaxy.datatypes.assembly DEBUG 2011-02-21 15:19:10,548 Velvet log info JJ __init__ galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer for datatype: galaxy.datatypes.binary:Bam galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer for datatype: galaxy.datatypes.binary:Sff galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer for datatype: galaxy.datatypes.xml:BlastXml galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer for datatype: galaxy.datatypes.sequence:Maf galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer for datatype: galaxy.datatypes.sequence:Lav galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer for datatype: galaxy.datatypes.sequence:csFasta galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,559 Loaded sniffer for datatype: galaxy.datatypes.qualityscore:QualityScoreSOLiD galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,560 Loaded sniffer for datatype: galaxy.datatypes.qualityscore:QualityScore454 galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,560 Loaded sniffer for datatype: galaxy.datatypes.sequence:Fasta galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,560 Loaded sniffer for datatype: galaxy.datatypes.sequence:Fastq galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,560 Loaded sniffer for datatype: galaxy.datatypes.interval:Wiggle galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,561 Loaded sniffer for datatype: galaxy.datatypes.images:Html galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,561 Loaded sniffer for datatype: galaxy.datatypes.images:Pdf galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,561 Loaded sniffer for datatype: galaxy.datatypes.sequence:Axt galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,561 Loaded sniffer for datatype: galaxy.datatypes.interval:Bed galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,561 Loaded sniffer for datatype: galaxy.datatypes.interval:CustomTrack galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,562 Loaded sniffer for datatype: galaxy.datatypes.interval:Gtf galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,562 Loaded sniffer for datatype: galaxy.datatypes.interval:Gff galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,562 Loaded sniffer for datatype: galaxy.datatypes.interval:Gff3 galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,562 Loaded sniffer for datatype: galaxy.datatypes.tabular:Pileup galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,562 Loaded sniffer for datatype: galaxy.datatypes.interval:Interval galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,563 Loaded sniffer for datatype: galaxy.datatypes.tabular:Sam galaxy.datatypes.registry DEBUG 2011-02-21 15:19:10,563 Loaded sniffer for datatype: galaxy.datatypes.tabular:Vcf galaxy.model.migrate.check DEBUG 2011-02-21 15:19:10,606 pysqlite>=2 egg successfully loaded for sqlite dialect Traceback (most recent call last): File "/Users/pjcock/repositories/galaxy-central/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/Users/pjcock/repositories/galaxy-central/lib/galaxy/app.py", line 32, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/Users/pjcock/repositories/galaxy-central/lib/galaxy/model/migrate/check.py", line 102, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest ) ) Exception: Your database has version '73' but this code expects version '75'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. $ sh manage_db.sh upgrade Traceback (most recent call last): File "./scripts/manage_db.py", line 12, in <module> from migrate.versioning.shell import main ImportError: No module named migrate.versioning.shell In case it is of use (it was asked for on what looked like a similar issue), $ ls lib/galaxy/model/migrate/versions/ 0001_initial_tables.py 0038_add_inheritable_column_to_library_template_assoc_tables.py 0001_initial_tables.pyc 0038_add_inheritable_column_to_library_template_assoc_tables.pyc 0002_metadata_file_table.py 0039_add_synopsis_column_to_library_table.py 0002_metadata_file_table.pyc 0039_add_synopsis_column_to_library_table.pyc 0003_security_and_libraries.py 0040_page_annotations.py 0003_security_and_libraries.pyc 0040_page_annotations.pyc 0004_indexes_and_defaults.py 0041_workflow_invocation.py 0004_indexes_and_defaults.pyc 0041_workflow_invocation.pyc 0005_cleanup_datasets_fix.py 0042_workflow_invocation_fix.py 0005_cleanup_datasets_fix.pyc 0042_workflow_invocation_fix.pyc 0006_change_qual_datatype.py 0043_visualization_sharing_tagging_annotating.py 0006_change_qual_datatype.pyc 0043_visualization_sharing_tagging_annotating.pyc 0007_sharing_histories.py 0044_add_notify_column_to_request_table.py 0007_sharing_histories.pyc 0044_add_notify_column_to_request_table.pyc 0008_galaxy_forms.py 0045_request_type_permissions_table.py 0008_galaxy_forms.pyc 0045_request_type_permissions_table.pyc 0009_request_table.py 0046_post_job_actions.py 0009_request_table.pyc 0046_post_job_actions.pyc 0010_hda_display_at_authz_table.py 0047_job_table_user_id_column.py 0010_hda_display_at_authz_table.pyc 0047_job_table_user_id_column.pyc 0011_v0010_mysql_index_fix.py 0048_dataset_instance_state_column.py 0011_v0010_mysql_index_fix.pyc 0048_dataset_instance_state_column.pyc 0012_user_address.py 0049_api_keys_table.py 0012_user_address.pyc 0049_api_keys_table.pyc 0013_change_lib_item_templates_to_forms.py 0050_drop_cloud_tables.py 0013_change_lib_item_templates_to_forms.pyc 0050_drop_cloud_tables.pyc 0014_pages.py 0051_imported_col_for_jobs_table.py 0014_pages.pyc 0051_imported_col_for_jobs_table.pyc 0015_tagging.py 0052_sample_dataset_table.py 0015_tagging.pyc 0052_sample_dataset_table.pyc 0016_v0015_mysql_index_fix.py 0053_item_ratings.py 0016_v0015_mysql_index_fix.pyc 0053_item_ratings.pyc 0017_library_item_indexes.py 0054_visualization_dbkey.py 0017_library_item_indexes.pyc 0054_visualization_dbkey.pyc 0018_ordered_tags_and_page_tags.py 0055_add_pja_assoc_for_jobs.py 0018_ordered_tags_and_page_tags.pyc 0055_add_pja_assoc_for_jobs.pyc 0019_request_library_folder.py 0056_workflow_outputs.py 0019_request_library_folder.pyc 0056_workflow_outputs.pyc 0020_library_upload_job.py 0057_request_notify.py 0020_library_upload_job.pyc 0057_request_notify.pyc 0021_user_prefs.py 0058_history_import_export.py 0021_user_prefs.pyc 0058_history_import_export.pyc 0022_visualization_tables.py 0059_sample_dataset_file_path.py 0022_visualization_tables.pyc 0059_sample_dataset_file_path.pyc 0023_page_published_and_deleted_columns.py 0060_history_archive_import.py 0023_page_published_and_deleted_columns.pyc 0060_history_archive_import.pyc 0024_page_slug_unique_constraint.py 0061_tasks.py 0024_page_slug_unique_constraint.pyc 0061_tasks.pyc 0025_user_info.py 0062_user_openid_table.py 0025_user_info.pyc 0062_user_openid_table.pyc 0026_cloud_tables.py 0063_sequencer_table.py 0026_cloud_tables.pyc 0063_sequencer_table.pyc 0027_request_events.py 0064_add_run_and_sample_run_association_tables.py 0027_request_events.pyc 0064_add_run_and_sample_run_association_tables.pyc 0028_external_metadata_file_override.py 0065_add_name_to_form_fields_and_values.py 0028_external_metadata_file_override.pyc 0065_add_name_to_form_fields_and_values.pyc 0029_user_actions.py 0066_deferred_job_and_transfer_job_tables.py 0029_user_actions.pyc 0066_deferred_job_and_transfer_job_tables.pyc 0030_history_slug_column.py 0067_populate_sequencer_table.py 0030_history_slug_column.pyc 0067_populate_sequencer_table.pyc 0031_community_and_workflow_tags.py 0068_rename_sequencer_to_external_services.py 0031_community_and_workflow_tags.pyc 0068_rename_sequencer_to_external_services.pyc 0032_stored_workflow_slug_column.py 0069_rename_sequencer_form_type.py 0032_stored_workflow_slug_column.pyc 0069_rename_sequencer_form_type.pyc 0033_published_cols_for_histories_and_workflows.py 0070_add_info_column_to_deferred_job_table.py 0033_published_cols_for_histories_and_workflows.pyc 0070_add_info_column_to_deferred_job_table.pyc 0034_page_user_share_association.py 0071_add_history_and_workflow_to_sample.py 0034_page_user_share_association.pyc 0071_add_history_and_workflow_to_sample.pyc 0035_item_annotations_and_workflow_step_tags.py 0072_add_pid_and_socket_columns_to_transfer_job_table.py 0035_item_annotations_and_workflow_step_tags.pyc 0072_add_pid_and_socket_columns_to_transfer_job_table.pyc 0036_add_deleted_column_to_library_template_assoc_tables.py 0073_add_ldda_to_implicit_conversion_table.py 0036_add_deleted_column_to_library_template_assoc_tables.pyc 0073_add_ldda_to_implicit_conversion_table.pyc 0037_samples_library.py 0074_add_purged_column_to_library_dataset_table.py 0037_samples_library.pyc 0075_add_subindex_column_to_run_table.py peter-cocks-mac-pro:galaxy-central pjcock$

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Re: [galaxy-dev] importing into history from library
by Jim Johnson 17 Mar '11

17 Mar '11

This is likely fixed in templates/library/common/browse_library.mako in the development source: https://bitbucket.org/galaxy/galaxy-central/changeset/5f5dae7e7ccc

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Re: [galaxy-dev] [galaxy-user] CpG Masking changing alignment length?
by Guru Ananda 17 Mar '11

17 Mar '11

Hi Michael, Apologies for the delay in response. The 'Mask CpG' tool currently supports pairwise alignments only, and it skips all blocks containing a single species. This is the reason why your masked output has fewer blocks compared to the input MAF file. We don't have immediate plans to extend the tool to >2-way alignments. If we are to do this, we'll let you know. Thanks for using Galaxy, and please let us know if you have any other questions. Guru. On Mon, Mar 14, 2011 at 10:02 AM, Michael E. Steiper < michaelsteiper(a)gmail.com> wrote: > Hi Guru > > I had a look at the maf files (I am new to them, so this is just my > guess). It looks like the maf to fasta in Galaxy removes all of the > blocks that have only one species present. Does this look like the > situation? Again, I am new to this file type. > > Thanks for looking into this for me. > > Best > > Mike > > > > On Mon, Mar 14, 2011 at 9:56 AM, Guru Ananda <guru(a)psu.edu> wrote: > > Hi Mike, > > It looks like 'Mask CpG' tool is returning 13064 blocks out of the 17209 > > blocks in your input MAF file. This is perhaps why the sequence lengths > > before and after masking differ. We are trying to identifying the source > of > > this issue. We'll keep you posted about the same. > > Sorry for any inconvenience this may have caused. > > Guru. > > On Thu, Mar 10, 2011 at 10:42 AM, Michael E. Steiper > > <michaelsteiper(a)gmail.com> wrote: > >> > >> Dear Guru, > >> Yes, of course. I just shared it with you. > >> Best > >> Mike > >> > >> On Thu, Mar 10, 2011 at 10:30 AM, Guru Ananda <guru(a)psu.edu> wrote: > >> > Hi Mike, > >> > Would you mind sharing your history with me (guru(a)psu.edu) so that I > can > >> > take a look at what's going on? You can do this by selecting "Options > >> > -> Share or Publish -> Share with a user" and entering my email > address. > >> > Thanks, > >> > Guru. > >> > > >> > On Thu, Mar 10, 2011 at 9:15 AM, Michael E. Steiper > >> > <michaelsteiper(a)gmail.com> wrote: > >> >> > >> >> Hi, > >> >> > >> >> Sorry, a correction (I had the lengths reversed): > >> >> > >> >> Original .maf > maf to fasta > length is 5572544 > >> >> Original .maf > CpG mask > maf to fasta > length is 2735329 > >> >> > >> >> Thanks, > >> >> > >> >> Mike > >> >> > >> >> On Thu, Mar 10, 2011 at 8:53 AM, Michael E. Steiper > >> >> <michaelsteiper(a)gmail.com> wrote: > >> >> > Hi All, > >> >> > > >> >> > I have a general question about CpG masking. I have a .maf file, > >> >> > when > >> >> > I use the maf to fasta tool, it gives me an alignment of 2,735,329 > >> >> > bp. > >> >> > But if I CpG mask the .maf file (restricted definition) then I use > >> >> > the maf to fasta tool, I get a very different alignment length, > >> >> > 5,572,544 bp. It would be great to know what is the cause of these > >> >> > differences. > >> >> > > >> >> > THANKS! > >> >> > > >> >> > Mike > >> >> > > >> >> > >> >> ___________________________________________________________ > >> >> 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/ > >> > > >> > > >> > > >> > -- > >> > Graduate student, Bioinformatics and Genomics > >> > Makova lab/Galaxy team > >> > 505 Wartik lab > >> > University Park PA 16802 > >> > guru(a)psu.edu > >> > > > > > > > > > -- > > Graduate student, Bioinformatics and Genomics > > Makova lab/Galaxy team > > 505 Wartik lab > > University Park PA 16802 > > guru(a)psu.edu > > > -- Graduate student, Bioinformatics and Genomics Makova lab/Galaxy team 505 Wartik lab University Park PA 16802 guru(a)psu.edu

1 0

purge and delete data
by Nicolas Servant 16 Mar '11

16 Mar '11

Dear Galaxy developers, I just started to configure and use Galaxy, and I don't really understand how we can delete/purge data from the disk. I delete several dataset or libraries from the admin interface and then run the script/cleanup_datasets scripts as explained in https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDa… (with the -d0 option) >From the interface my libraries are flagged purged as expected ... but on the disk I still have the files ! how can I remove these files from the disk ? Another question, the purged libraries are still available through the advanced search - deleted, how can I completely remove these libraries from Galaxy ? Thanks for your help, Regards, Nicolas -- Nicolas Servant Equipe Bioinformatique Institut Curie 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE Email: Nicolas.Servant(a)curie.fr Tel: 01 56 24 69 85 http://bioinfo.curie.fr/

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galaxy-cloud display data in browser broken
by Isabelle Phan 16 Mar '11

16 Mar '11

Hello, Running galaxy-cloud latest release on amazon EC2, configuration out of the box except for: host = 0.0.0.0 I can upload data, run tools, but when I click on the 'eye' icon to view the data , the middle panel is empty (accessing galaxy cloud from Firefox and Chrome on CentOS linux). I tried creating a simple fasta file. It shows fine on the right panel, but won't display in the middle panel. View parameters displays correctly. Only the actual data is not displayed. The log shows no error: 146.129.249.238 - - [10/Mar/2011:02:19:52 +0000] "GET /datasets/5969b1f7201f12ae/display/?preview=True HTTP/1.1" 200 - "http://ec2-xxxxxx.compute-1.amazonaws.com:8080/history?show_deleted=False" "Mozilla/5.0 (X11; Linux i686 (x86_64)) AppleWebKit/534.24 (KHTML, like Gecko) Chrome/11.0.697.0 Safari/534.24" Our local instance of Galaxy does not have this issue, only the cloud instance. Since this is a total blocker, any hint is *very* gratefully received, Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113

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Applet and path concerns (local instance)
by Bonci, Timothy Daniel 16 Mar '11

16 Mar '11

I currently have a Python script that outputs an HTML with an embedded Applet. The Java is installed under /tools/blah and I have the <Applet archive=../../../tools/blah> which should appropriately step out of the dataset space where the HTML wants to execute, but it returns 404's for the code. Is there something I am doing wrong? How can a returned HTML properly access the files I need? ---Tim Bonci

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