Architecture 14 - Galaxy Startup Process

Contributors

John Chilton

Questions

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

Objectives

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

last_modification Published: Feb 19, 2026

last_modification Last Updated: Feb 19, 2026

Architecture 14 - Galaxy Startup Process

The architecture of Galaxy’s initialization.

layout: true left-aligned class: left, middle — layout: true class: center, middle

Cloning Galaxy

$ git clone 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

.code[``` 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 (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 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 (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 (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 (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



---


class: reduce70

### Initial Debugging as App Starts

.code[```
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
```]


---


class: reduce70

### Database Migrations (First Time Only)

.code[```
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


---


class: reduce70

### Loading Tool Shed Migrations

.code[```
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.
```]


---


class: reduce70

### Loading Datatypes

.code[```
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.
```]


---


class: reduce70

### Loading Datatype Sniffers

.code[```
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

.code[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

.code[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

.code[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

.code[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

.code[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

.code[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

.code[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

.code[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

.code[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

.code[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

.code[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

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

Loading Controllers

.code[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

.code[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

.code[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!

.code[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]

Next: Galaxy Production Deployment]

Key Points

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

Thank you!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors!

Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.

Architecture 14 - Galaxy Startup Process

Contributors

Questions

Objectives

Architecture 14 - Galaxy Startup Process

Cloning Galaxy

Copying Configs

Setting up .venv and pip

Installing Dependencies

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 Points

Thank you!

Setting up `.venv` and `pip`