February 2011 - galaxy-dev - lists.galaxyproject.org

Output file naming / dataset's label
by Tanguy Le Carrour 14 Apr '11

14 Apr '11

Dear Galaxy Team, I started using Galaxy few months ago. I'm now setting up my first "real" workflows. I would like to keep the name of my input file through the various steps as dataset's label, maybe also modify it a bit, and finally give a "proper" name to the result file downloaded. A simple example: 1) date-sample_name.gff3 --[step1]-> date-sample_name-step1.tsv 2) date-sample_name-step1.tsv --[step2]-> date-sample_name-step1-step2.txt 3 download date-sample_name-step1-step2.txt I've seen that I can use the 'label' attribute in the tool config "data" tag to do so. But I don't know how to access the ${input.label} (?) and how to modify it. I doesn't stop me using my workflows, but it would definitely help my users not to get lost when they use them. Best regards, Tanguy Le Carrour -- Tanguy LE CARROUR Functional Genomics Center Zurich ETH Zurich / University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland

4 8

2011 Galaxy Community Conference, May 25-26, Lunteren, The Netherlands
by Dave Clements 11 Apr '11

11 Apr '11

Hello all, We are pleased to announce the *2011 Galaxy Community Conference*, being held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your own and your community's research. *Link: http://galaxy.psu.edu/gcc2011/ * *Overview *This event aims to engage a broader community of developers, data producers, tool creators, and core facility and other research hub staff to become an active part of the Galaxy community. We'll cover defining resources in the Galaxy framework, increasing their visibility and making them easier to use and integrate with other resources, how to extend Galaxy to use custom data sources and custom tools, and best practices for using Galaxy in your organization. Additional topics include, but are not limited to: * Talks submitted by the Galaxy community * Integration of tools (including NGS analysis tools) and distributed job management * Deployment of Galaxy instances on local resources and on the Cloud * Management of large datasets with the Galaxy Library System * Using the Galaxy LIMS functionality at NGS sequencing facilities * Visualizing Data without leaving Galaxy * Performing reproducible research * Performing and sharing complex analyses with Workflows * An "Introduction to Galaxy" session, offered on May 24, for Galaxy newcomers. *Registration *The conference fee is €100 on or before April 24, and €120 after that. The meeting is being held at the Conference Centre De Werelt in Lunteren, The Netherlands, which is also the conference hotel. You are encouraged to register early, as space at the hotel (and at the "Intro to Galaxy" session) is limited and is likely to fill up before the conference itself does. *Link: http://galaxy.psu.edu/gcc2011/Register.html ** Abstract Submission *Abstracts are now being accepted for short oral presentations. Proposals on any topic of interest to the Galaxy community are welcome and encouraged. The abstract submission deadline is the end of February 28. *Link: http://galaxy.psu.edu/gcc2011/Abstracts.html * *Sponsors *The 2011 Galaxy Community Conference is co-sponsored by the US National Science Foundation (NSF), and the Netherlands Bioinformatics Centre (NBIC). NBIC is a collaborative institute of the bioinformatics groups in the Netherlands. Together, these groups perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. *Links: http://www.nbic.nl/ and http://www.nsf.gov/ * We are looking forward to a great conference and hope to see you in the Netherlands! The Galaxy and NBIC Teams -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

2 2

Restricted user builds
by Dan MacLean (TSL) 28 Mar '11

28 Mar '11

Dear Galaxy, We have an internal installation of Galaxy running very nicely with a fair number of internally generated builds and plenty of data libraries, recently a user asked if it was possible to add a build and restrict to just a few users. Is this possible? I couldn't find any specific documentation on the subject. Thanks for any help Dan

2 1

swap issue
by Isabelle Phan 22 Mar '11

22 Mar '11

Hello, I am running galaxy, using a postgres backend. The galaxy server systematically gets killed whenever I try uploading a bam file. The samtools process is still running. This is the end of the log: 2010-08-26 18:08:11,371 INFO sqlalchemy.engine.threadlocal.TLEngine.0x...4610 {'param_1': 8} sqlalchemy.engine.threadlocal.TLEngine.0x...4610 INFO 2010-08-26 18:08:11,371 {'param_1': 8} 2010-08-26 18:08:11,378 INFO sqlalchemy.pool.QueuePool.0x...4ed0 Connection <connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var closed: 0> being returned to pool sqlalchemy.pool.QueuePool.0x...4ed0 INFO 2010-08-26 18:08:11,378 Connection <connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var closed: 0> being returned to pool 10.1.20.44 - - [26/Aug/2010:18:08:06 -0700] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy:8080/history" "Mozilla/5.0 (X1 (x86_64); en-US; rv:1.9.2.8) Gecko/20100722 Firefox/3.6.8" Killed I have the following options set in universe_wsgi.ini: database_engine_option_server_side_cursors = True database_engine_option_strategy = threadlocal It seems to be running out of swap. I monitored memory usage with 'top' and galaxy died when available swap hit 0k free. I am not superuser on the machine where galaxy is running and I have no other server available. Is there something I could do to prevent galaxy from dying? Thanks, Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113

3 4

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$

2 8

Running a workflow programatically
by Darren Brown 15 Mar '11

15 Mar '11

Hello folks, I am using a workflow that needs to be run many times on many different inputs. I have hacked around and figured out how to pull multiple inputs from a history, but I am a little baffled on how to run a galaxy workflow programatically. I have searched around fairly exhaustively and am wondering if this is something that anyone else has come across and accomplished. And links or pointers? Take care, Darren

2 6

fastq filetypes
by Ryan Golhar 07 Mar '11

07 Mar '11

Is there a way to quickly determine what fastq filetype a particular fastq file is? I ask because I was recently given a fastq which which I incorrectly assumed to be fastqsanger. When I ran a fastx tool on the file, the tool seg faulted. It took me a while to figure out that the fastq type is not sanger. Is there a tool available that report what the encoding type is? -- 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.

2 1

possible bug - user log in / browser cache
by Ryan Golhar 07 Mar '11

07 Mar '11

I have a local instance running. When I'm logged in as user1, log out, then try to log in as user2, I keep getting the "You have been logged out" message. Its as if the browser's cache is retaining some information. To get around this, after I log out as user1, I have to click on Analyze Data, then click on Log in to log in as user2. I'm running Safari on Mac, but have noticed this with Firefox as well.

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file upload
by Musa A. Hassan 07 Mar '11

07 Mar '11

I am trying to use galaxy for the first time and am running into some early problems. While trying to upload my file which is basically an fq containing illumina short reads, the file won't upload. When I try the fastq extension of the same file, it does but then the file isn't recognized by the galaxy hence it's like I have no file uploaded. Does anyone have an idea what's going on here. I've looked at the short tutorial on galaxy and it seems my file should be fine. Musa

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phastCons and phastOdds scores
by David Hoover 04 Mar '11

04 Mar '11

Does anyone have a clear explanation of what files are required/available for Get Genomic Scores -> Aggregate datapoints, Compute phastOdds (binned_scores.loc and phastOdds.loc files)? I know there are .mod and .pp files and .wigFix files from UCSC, but I can't figure out exactly what Galaxy is looking for. Do I need to install PHAST and generate these score files? David Hoover Helix Systems Staff http://helix.nih.gov

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