Galaxy Startup Process

📊 View as slides

Learning Questions

What happens when Galaxy starts?
What is the startup sequence?
What gets loaded during startup?

Learning Objectives

Understand the Galaxy startup sequence
Learn about configuration initialization
Understand dependency installation
Learn about database migrations and plugin loading

Cloning Galaxy

$ git clone [https://github.com/galaxyproject/galaxy.git](https://github.com/galaxyproject/galaxy.git) galaxy
Cloning into 'galaxy'...
remote: Counting objects: 173809, done.
remote: Total 173809 (delta 0), reused 0 (delta 0), pack-reused 173809
Receiving objects: 100% (173809/173809), 55.18 MiB | 11.08 MiB/s, done.
Resolving deltas: 100% (137885/137885), done.
Checking connectivity... done.
$ cd galaxy
$ git checkout -b master origin/master
Branch master set up to track remote branch master from origin.
Switched to a new branch 'master'
$ sh run.sh

Copying Configs

$ sh run.sh
Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample
Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample
Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample
Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample
Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample
Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample
Initializing tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample
Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample
Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample
Initializing static/welcome.html from welcome.html.sample

Setting up `.venv` and `pip`

Using real prefix '/usr'
New python executable in .venv/bin/python
Installing setuptools, pip, wheel...done.
Activating virtualenv at .venv
Collecting pip>=8.1
  Using cached pip-8.1.2-py2.py3-none-any.whl
Installing collected packages: pip
  Found existing installation: pip 7.1.2
    Uninstalling pip-7.1.2:
      Successfully uninstalled pip-7.1.2
Successfully installed pip-8.1.2

Installing Dependencies

Collecting bx-python==0.7.3 (from -r requirements.txt (line 2))
  Downloading [https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27mu-manylinux1_x86_64.whl](https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27mu-manylinux1_x86_64.whl) (2.1MB)
Collecting MarkupSafe==0.23 (from -r requirements.txt (line 3))
  Downloading [https://wheels.galaxyproject.org/packages/MarkupSafe-0.23-cp27-cp27mu-manylinux1_x86_64.whl](https://wheels.galaxyproject.org/packages/MarkupSafe-0.23-cp27-cp27mu-manylinux1_x86_64.whl)
Collecting PyYAML==3.11 (from -r requirements.txt (line 4))
  Downloading [https://wheels.galaxyproject.org/packages/PyYAML-3.11-cp27-cp27mu-manylinux1_x86_64.whl](https://wheels.galaxyproject.org/packages/PyYAML-3.11-cp27-cp27mu-manylinux1_x86_64.whl) (367kB)
Collecting SQLAlchemy==1.0.8 (from -r requirements.txt (line 5))
  Downloading [https://wheels.galaxyproject.org/packages/SQLAlchemy-1.0.8-cp27-cp27mu-manylinux1_x86_64.whl](https://wheels.galaxyproject.org/packages/SQLAlchemy-1.0.8-cp27-cp27mu-manylinux1_x86_64.whl) (1.0MB)
Collecting mercurial==3.7.3 (from -r requirements.txt (line 6))
  Downloading [https://wheels.galaxyproject.org/packages/mercurial-3.7.3-cp27-cp27mu-manylinux1_x86_64.whl](https://wheels.galaxyproject.org/packages/mercurial-3.7.3-cp27-cp27mu-manylinux1_x86_64.whl) (1.5MB)
...
...
Building wheels for collected packages: repoze.lru
  Running setup.py bdist_wheel for repoze.lru: started
  Running setup.py bdist_wheel for repoze.lru: finished with status 'done'
  Stored in directory: /home/john/.cache/pip/wheels/b2/cd/b3/7e24400bff83325a01d492940eff6e9579f553f33348323d79
Successfully built repoze.lru
Installing collected packages: bx-python, MarkupSafe, PyYAML, SQLAlchemy, mercurial, numpy, pycrypto, six, Paste, PasteDeploy, docutils, wchartype, repoze.lru, Routes, WebOb, WebHelpers, Mako, pytz, Babel, Beaker, dictobj, nose, Parsley, Whoosh, Markdown, Cheetah, requests, boto, requests-toolbelt, bioblend, anyjson, amqp, kombu, psutil, PasteScript, pulsar-galaxy-lib, sqlparse, pbr, decorator, Tempita, sqlalchemy-migrate, pyparsing, svgwrite, ecdsa, paramiko, Fabric, pysam
Successfully installed Babel-2.0 Beaker-1.7.0 Cheetah-2.4.4 Fabric-1.10.2 Mako-1.0.2 Markdown-2.6.3 MarkupSafe-0.23 Parsley-1.3 Paste-2.0.2 PasteDeploy-1.5.2 PasteScript-2.0.2 PyYAML-3.11 Routes-2.2 SQLAlchemy-1.0.8 Tempita-0.5.3.dev0 WebHelpers-1.3 WebOb-1.4.1 Whoosh-2.7.4 amqp-1.4.8 anyjson-0.3.3 bioblend-0.7.0 boto-2.38.0 bx-python-0.7.3 decorator-4.0.2 dictobj-0.3.1 docutils-0.12 ecdsa-0.13 kombu-3.0.30 mercurial-3.7.3 nose-1.3.7 numpy-1.9.2 paramiko-1.15.2 pbr-1.8.0 psutil-4.1.0 pulsar-galaxy-lib-0.7.0.dev4 pycrypto-2.6.1 pyparsing-2.1.1 pysam-0.8.4+gx1 pytz-2015.4 repoze.lru-0.6 requests-2.8.1 requests-toolbelt-0.4.0 six-1.9.0 sqlalchemy-migrate-0.10.0 sqlparse-0.1.16 svgwrite-1.1.6 wchartype-0.1

Initial Debugging as App Starts

Activating virtualenv at .venv
DEBUG:galaxy.app:python path is: /home/john/workspace/galaxy-clean/scripts,
/home/john/workspace/galaxy-clean/lib, /home/john/workspace/galaxy-clean/.venv/lib/python2.7,/home/john/workspace/galaxy-clean/.venv/lib/python2.7/plat-x86_64-linux-gnu,
/home/john/workspace/galaxy-clean/.venv/lib/python2.7/lib-tk, /home/john/workspace/galaxy-clean/.venv/lib/python2.7/lib-old, /home/john/workspace/galaxy-clean/.venv/lib/python2.7/lib-dynload,
/usr/lib/python2.7, /usr/lib/python2.7/plat-x86_64-linux-gnu, /usr/lib/python2.7/lib-tk, /home/john/workspace/galaxy-clean/.venv/local/lib/python2.7/site-packages
INFO:galaxy.config:Logging at '10' level to 'stdout'
galaxy.queue_worker INFO 2016-06-23 19:11:51,925 Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE
tool_shed.tool_shed_registry DEBUG 2016-06-23 19:11:51,951 Loading references to tool sheds from ./config/tool_sheds_conf.xml.sample
tool_shed.tool_shed_registry DEBUG 2016-06-23 19:11:51,951 Loaded reference to tool shed: Galaxy Main Tool Shed
galaxy.app DEBUG 2016-06-23 19:11:51,956 Using "galaxy.yml" config file:
/home/john/workspace/galaxy-clean/config/galaxy.yml.sample

Database Migrations (First Time Only)

migrate.versioning.repository DEBUG 2016-06-23 19:11:51,993 Loading repository lib/galaxy/model/migrate...
migrate.versioning.script.base DEBUG 2016-06-23 19:11:51,994 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py...
migrate.versioning.script.base DEBUG 2016-06-23 19:11:51,994 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2016-06-23 19:11:51,994 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py...
migrate.versioning.script.base DEBUG 2016-06-23 19:11:52,009 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py...
...
galaxy.model.migrate.check INFO 2016-06-23 19:13:32,812 Migrating 128 -> 129...
galaxy.model.migrate.check INFO 2016-06-23 19:13:33,436
galaxy.model.migrate.check INFO 2016-06-23 19:13:33,437 Migration script to allow invalidation of job external output metadata temp files
galaxy.model.migrate.check INFO 2016-06-23 19:13:33,437
galaxy.model.migrate.check INFO 2016-06-23 19:13:33,437
galaxy.model.migrate.check INFO 2016-06-23 19:13:33,437 Migrating 129 -> 130...
galaxy.model.migrate.check INFO 2016-06-23 19:13:34,325
galaxy.model.migrate.check INFO 2016-06-23 19:13:34,325 Migration script to change the value column of user_preference from varchar to text.
galaxy.model.migrate.check INFO 2016-06-23 19:13:34,325
galaxy.model.migrate.check INFO 2016-06-23 19:13:34,325
galaxy.model.migrate.check INFO 2016-06-23 19:13:34,326 Migrating 130 -> 131...
galaxy.model.migrate.check INFO 2016-06-23 19:13:35,633
galaxy.model.migrate.check INFO 2016-06-23 19:13:35,633 Migration script to support subworkflows and workflow request input parameters
galaxy.model.migrate.check INFO 2016-06-23 19:13:35,633
galaxy.model.migrate.check INFO 2016-06-23 19:13:35,633

Everything after here happens every time

Loading Tool Shed Migrations

migrate.versioning.repository DEBUG 2016-06-23 19:13:35,635 Loading repository lib/tool_shed/galaxy_install/migrate...
migrate.versioning.script.base DEBUG 2016-06-23 19:13:35,635 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py...
migrate.versioning.script.base DEBUG 2016-06-23 19:13:35,636 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2016-06-23 19:13:35,636 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py...
migrate.versioning.script.base DEBUG 2016-06-23 19:13:35,636 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2016-06-23 19:13:35,636 Loading script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py...
migrate.versioning.script.base DEBUG 2016-06-23 19:13:35,636 Script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py loaded successfully
...
migrate.versioning.repository DEBUG 2016-06-23 19:13:35,637 Repository lib/tool_shed/galaxy_install/migrate loaded successfully
tool_shed.galaxy_install.migrate.check DEBUG 2016-06-23 19:13:35,660 The main Galaxy tool shed is not currently available, so skipped tool migration 1 until next server startup
galaxy.config INFO 2016-06-23 19:13:35,679 Install database targetting Galaxy's database configuration.

Loading Datatypes

galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,748 Loading datatypes from ./config/datatypes_conf.xml.sample
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,749 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,750 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry.
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,751 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry.
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,751 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry.
...
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,822 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,822 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,824 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry.
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,824 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry.

Loading Datatype Sniffers

galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,824 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund'
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,824 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu'
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,824 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund'
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,824 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap'
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,824 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix'
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,824 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix'
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,825 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix'
...
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,826 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,826 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite'
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,833 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels'

Loading Build Sites

galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,833 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,834 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,834 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,834 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,834 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:35,834 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt

Loading Tool Data Tables

galaxy.tools.data INFO 2016-06-23 19:13:35,871 Could not find tool data tool-data/all_fasta.loc, reading sample
galaxy.tools.data DEBUG 2016-06-23 19:13:35,871 Loaded tool data table 'all_fasta'
galaxy.tools.data INFO 2016-06-23 19:13:35,871 Could not find tool data tool-data/bfast_indexes.loc, reading sample
galaxy.tools.data DEBUG 2016-06-23 19:13:35,871 Loaded tool data table 'bfast_indexes'
galaxy.tools.data WARNING 2016-06-23 19:13:35,871 Cannot find index file 'tool-data/blastdb_p.loc' for tool data table 'blastdb_p'
...
galaxy.tools.data DEBUG 2016-06-23 19:13:36,210 Loaded tool data table 'vcf_iobio'
galaxy.tools.data INFO 2016-06-23 19:13:36,211 Could not find tool data tool-data/biom_simple_display.loc, reading sample
galaxy.tools.data DEBUG 2016-06-23 19:13:36,211 Loaded tool data table 'biom_simple_display'

Job Configuration and Citation Cache

galaxy.jobs DEBUG 2016-06-23 19:13:36,233 Loading job configuration from /home/john/workspace/galaxy-clean/config/galaxy.yml.sample
galaxy.jobs DEBUG 2016-06-23 19:13:36,233 Done loading job configuration
beaker.container DEBUG 2016-06-23 19:13:36,278 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache

Loading Toolbox

galaxy.tools.toolbox.base INFO 2016-06-23 19:13:36,279 Parsing the tool configuration ./config/tool_conf.xml.sample
galaxy.tools.toolbox.base DEBUG 2016-06-23 19:13:36,291 Loaded tool id: upload1, version: 1.1.4 into tool panel..
galaxy.tools.toolbox.base DEBUG 2016-06-23 19:13:36,294 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2016-06-23 19:13:36,296 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base DEBUG 2016-06-23 19:13:36,298 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel..
...
galaxy.tools.toolbox.base DEBUG 2016-06-23 19:13:36,496 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel..
galaxy.tools.toolbox.base INFO 2016-06-23 19:13:36,497 Parsing the tool configuration ./config/shed_tool_conf.xml
galaxy.tools.toolbox.base INFO 2016-06-23 19:13:36,497 Parsing the tool configuration ./config/migrated_tools_conf.xml

Tool Dependency Resolution and Indexing

galaxy.tools.deps WARNING 2016-06-23 19:13:36,498 Path './database/dependencies' does not exist, ignoring
galaxy.tools.deps WARNING 2016-06-23 19:13:36,498 Path './database/dependencies' is not directory, ignoring
galaxy.tools.deps DEBUG 2016-06-23 19:13:36,503 Unable to find config file './dependency_resolvers_conf.xml'
galaxy.tools.search DEBUG 2016-06-23 19:13:36,560 Starting to build toolbox index.
galaxy.tools.search DEBUG 2016-06-23 19:13:37,789 Toolbox index finished. It took: 0:00:01.229406

Loading Display Applications

galaxy.datatypes.registry DEBUG 2016-06-23 19:13:37,795 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:37,797 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:37,833 Loaded display application 'igv_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:37,834 Loaded display application 'igb_bam' for datatype 'bam', inherit=False.
...
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:38,003 Adding inherited display application 'ensembl_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:38,007 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6'

Loading Datatype Converters

galaxy.datatypes.registry DEBUG 2016-06-23 19:13:38,010 Loaded converter: CONVERTER_Bam_Bai_0
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:38,011 Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:38,012 Loaded converter: CONVERTER_bed_to_gff_0
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:38,012 Loaded converter: CONVERTER_bed_to_bgzip_0
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:38,013 Loaded converter: CONVERTER_bed_to_tabix_0
...
galaxy.datatypes.registry DEBUG 2016-06-23 19:13:38,099 Loaded converter: CONVERTER_ref_to_seq_taxomony

Loading Special Tools

galaxy.datatypes.registry DEBUG 2016-06-23 19:13:38,101 Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2016-06-23 19:13:38,107 Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2016-06-23 19:13:38,108 Loaded history export tool: __EXPORT_HISTORY__

Loading Visualization Plugins

galaxy.web.base.pluginframework INFO 2016-06-23 19:13:38,109 VisualizationsRegistry, loaded plugin: charts
galaxy.visualization.plugins.config_parser INFO 2016-06-23 19:13:38,110 Visualizations plugin disabled: Circster. Skipping...
galaxy.web.base.pluginframework INFO 2016-06-23 19:13:38,111 VisualizationsRegistry, loaded plugin: csg
galaxy.web.base.pluginframework INFO 2016-06-23 19:13:38,112 VisualizationsRegistry, loaded plugin: graphviz
galaxy.web.base.pluginframework INFO 2016-06-23 19:13:38,112 VisualizationsRegistry, loaded plugin: phyloviz
galaxy.web.base.pluginframework INFO 2016-06-23 19:13:38,113 VisualizationsRegistry, loaded plugin: scatterplot
galaxy.web.base.pluginframework INFO 2016-06-23 19:13:38,114 VisualizationsRegistry, loaded plugin: trackster

Loading Tours

galaxy.tours INFO 2016-06-23 19:13:38,125 Loaded tour 'core.scratchbook'
galaxy.tours INFO 2016-06-23 19:13:38,158 Loaded tour 'core.galaxy_ui'
galaxy.tours INFO 2016-06-23 19:13:38,183 Loaded tour 'core.history'

Starting Job Handler and Runners

galaxy.jobs.manager DEBUG 2016-06-23 19:13:38,196 Starting job handler
galaxy.jobs INFO 2016-06-23 19:13:38,196 Handler 'main' will load all configured runner plugins
galaxy.jobs.runners.state_handler_factory DEBUG 2016-06-23 19:13:38,198 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs.runners DEBUG 2016-06-23 19:13:38,198 Starting 5 LocalRunner workers
galaxy.jobs DEBUG 2016-06-23 19:13:38,200 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
galaxy.jobs.handler DEBUG 2016-06-23 19:13:38,200 Loaded job runners plugins: local
galaxy.jobs.handler INFO 2016-06-23 19:13:38,200 job handler stop queue started
galaxy.jobs.handler INFO 2016-06-23 19:13:38,222 job handler queue started

Starting Workflow Scheduler

galaxy.workflow.scheduling_manager DEBUG 2016-06-23 19:13:38,254 Starting workflow schedulers

Loading Controllers

galaxy.web.framework.base DEBUG 2016-06-23 19:13:38,347 Enabling 'external_service' controller, class: ExternalService
galaxy.web.framework.base DEBUG 2016-06-23 19:13:38,347 Enabling 'requests_common' controller, class: RequestsCommon
galaxy.web.framework.base DEBUG 2016-06-23 19:13:38,375 Enabling 'library_common' controller, class: LibraryCommon
galaxy.web.framework.base DEBUG 2016-06-23 19:13:38,390 Enabling 'visualization' controller, class: VisualizationController
...
galaxy.web.framework.base DEBUG 2016-06-23 19:13:38,728 Enabling 'workflow_tags' API controller, class: WorkflowTagsController

Enabling Middleware

galaxy.webapps.galaxy.buildapp DEBUG 2016-06-23 19:13:39,036 Enabling 'httpexceptions' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2016-06-23 19:13:39,037 Enabling 'recursive' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2016-06-23 19:13:39,042 Enabling 'error' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2016-06-23 19:13:39,043 Enabling 'trans logger' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2016-06-23 19:13:39,044 Enabling 'x-forwarded-host' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2016-06-23 19:13:39,044 Enabling 'Request ID' middleware

Configuring Static Paths

galaxy.webapps.galaxy.buildapp DEBUG 2016-06-23 19:13:39,048 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static
galaxy.webapps.galaxy.buildapp DEBUG 2016-06-23 19:13:39,048 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static
galaxy.webapps.galaxy.buildapp DEBUG 2016-06-23 19:13:39,049 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static
galaxy.webapps.galaxy.buildapp DEBUG 2016-06-23 19:13:39,049 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static

Galaxy is Ready!

galaxy.queue_worker INFO 2016-06-23 19:13:39,049 Binding and starting galaxy control worker for main
Starting server in PID 21102.
serving on [http://127.0.0.1:8080](http://127.0.0.1:8080)

Key Takeaways

Startup: clone, config copy, venv, dependencies, migrations
Datatypes, tools, and plugins loaded at startup
Database migrations run on first startup
Default setup ‘just works’ for development

Galaxy Startup Process

Learning Questions

Learning Objectives

Cloning Galaxy

Copying Configs

Setting up .venv and pip

Installing Dependencies

Initial Debugging as App Starts

Database Migrations (First Time Only)

Loading Tool Shed Migrations

Loading Datatypes

Loading Datatype Sniffers

Loading Build Sites

Loading Tool Data Tables

Job Configuration and Citation Cache

Loading Toolbox

Tool Dependency Resolution and Indexing

Loading Display Applications

Loading Datatype Converters

Loading Special Tools

Loading Visualization Plugins

Loading Tours

Starting Job Handler and Runners

Starting Workflow Scheduler

Loading Controllers

Enabling Middleware

Configuring Static Paths

Galaxy is Ready!

Key Takeaways

Setting up `.venv` and `pip`