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$