on infrastructure clouds. Main component of Galaxy cloud images github.com/galaxyproject/ cloudlaunch CloudLaunch web application to make it easy to launch images on a cloud, drives http: //launch.usegalaxy.org
and iuc (the “Intergalactic Utilities Commission”). A variety of tools, generally of high quality, including the core tools for Galaxy main. Demonstrates current tool development best practices - development on github and then deployed to test/main ToolSheds.
of Galaxy tools. Linting, testing, deploying to ToolSheds… The best practice approach for Galaxy tool development! github.com/galaxyproject/ planemo-machine Builds Galaxy environments for Galaxy tool development including Docker containers, virtual machines, Google compute images...
of Galaxy installation and maintenance. Ansible is an advanced configuration management system These playbooks are used to maintain Galaxy main, cloud images, virtual machines, ...
API: RESTful HTTP API for accessing and controlling the Galaxy application Managers: Manage resources in the scope of a user transaction, abstract most logic out of controllers Models: encapsulate all persistent state (except for raw data) – users, metadata, workflows, … persisted to relational database (ideally postgres) using SQLAlchemy layer Execution: Getting jobs run. Managing possibly a wide variety of different execution engines behind a single Galaxy instance.
Tool shed *Many of these have an API but it is not yet used by the UI The new way Visualizations History Tool menu Most grids In between Workflows Data Libraries
Tool shed *Many of these have an API but it is not yet used by the UI The new way Visualizations History Tool menu Most grids In between Workflows Data Libraries (beta)
defined in galaxy.model as objects SQLAlchemy is used for object relation mapping Mappings are defined in galaxy.model.mapping in two parts — a table definition and a mapping between objects and tables including relationships Migrations allow the schema to be migrated forward automatically
my viz? - Framework provides direct link to read the raw dataset - or use Data providers - In config, assert that visualization requires a given type of data providers - Data providers process data before sending to browser. Slice, filter, reformat, ...
and base template - Within the base template, launch a Docker container running a web accessible process - Build a UI that accesses that process through a proxy
how do you get a handle on them? - Group datasets into a single unit - Perform complex operations on that unit - Operations are performed on each group element - Output of each operation is a new group
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 lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml from user_info.xml.sample Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample Initializing tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample . . . Initializing tool-data/sift_db.loc from sift_db.loc.sample Initializing tool-data/srma_index.loc from srma_index.loc.sample Initializing tool-data/twobit.loc from twobit.loc.sample Initializing static/welcome.html from welcome.html.sample * There are many more configs in the configs/ directory, used in their “.sample” state. shed_* are mutable configs. Start hacking with: cp galaxy.ini.sample galaxy.ini
attempting to fetch... Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg Fetched http://eggs.galaxyproject.org/repoze.lru/repoze.lru-0.6-py2.7.egg Fetched http://eggs.galaxyproject.org/pycrypto/pycrypto-2.5-py2.7-linux-x86_64-ucs4.egg Fetched http://eggs.galaxyproject.org/boto/boto-2.27.0-py2.7.egg Fetched http://eggs.galaxyproject.org/Paste/Paste-1.7.5.1-py2.7.egg Fetched http://eggs.galaxyproject.org/wsgiref/wsgiref-0.1.2-py2.7.egg . . . Fetched http://eggs.galaxyproject.org/pytz/pytz-2013.9-py2.7.egg Fetched http://eggs.galaxyproject.org/nose/nose-0.11.1-py2.7.egg Fetched http://eggs.galaxyproject.org/requests/requests-2.2.1-py2.7.egg Fetched http://eggs.galaxyproject.org/anyjson/anyjson-0.3.3-py2.7.egg Fetched http://eggs.galaxyproject.org/WebError/WebError-0.8a-py2.7.egg Fetched http://eggs.galaxyproject.org/twill/twill-0.9-py2.7.egg Fetch successful. * As a result of this year’ s GCC Hackathon, eggs will soon be replaced by wheels, and will be installed the usual Pythonic way (with pip)
"./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/home/nate/galaxy-stable/config/galaxy.ini.sample" instead galaxy.jobs DEBUG 2015-07-06 06:46:14,022 Loading job configuration from /home/nate/galaxy-stable/config/galaxy. ini.sample galaxy.jobs DEBUG 2015-07-06 06:46:14,022 Done loading job configuration * config/job_conf.xml will automatically be read if created, see job_conf.xml.sample_advanced for fully documented examples of all possible configurations
./config/tool_conf.xml.sample galaxy.tools.toolbox.base DEBUG 2015-07-06 06:46:14,132 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2015-07-06 06:46:14,133 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. . . . galaxy.tools.toolbox.base DEBUG 2015-07-06 06:46:14,276 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base DEBUG 2015-07-06 06:46:14,278 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.. galaxy.tools.toolbox.base INFO 2015-07-06 06:46:14,278 Parsing the tool configuration ./config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2015-07-06 06:46:14,278 Parsing the tool configuration ./config/migrated_tools_conf. xml galaxy.tools.search DEBUG 2015-07-06 06:46:14,304 Starting to build toolbox index. galaxy.tools.search DEBUG 2015-07-06 06:46:14,890 Toolbox index finished. * shed_tool_conf.xml is empty on the first run so only tools provided with Galaxy are loaded, but after tools are installed from the Tool Shed, they will load here
80 - WSGI server is responsible for picking up the connection, parsing HTTP headers, and reformatting them into a dictionary according to the WSGI spec, this dict is called “environ” - In a default Galaxy install this is currently Paste#http
def app( environ, start_response ): … - Middleware act as filters, modify the environ and then pass through to the next webapp - Galaxy uses several middleware components galaxy.webapps.galaxy.buildapp#wrap_in_middleware error handling, logging, proxy hostname, debug, static, ...
of ideas with Pylons - __call__ method supports the WSGI spec - Takes environ and creates a wrapper object GalaxyWebTransaction -- this is the ubiquitous trans! - Parses path_info from the environment to determine what controller method to call. The mapping approach is implemented by a library called Routes that maps
matches the route pattern, so: lookup the controller named “dataset” look for a method named “display” that is exposed call it, passing dataset_id and filename as keyword args
methods accept trans as their first argument and additional keyword arguments By default, any <name>.py in the webapps controllers directory is loaded as controller <name> Can return a file or any iterable which will be streamed to the browser Often a helper like self.fill_template is used
starting with “/api” Should only return JSON All new functionality should be implemented using API controllers, eventually most or all non-API controllers will be eliminated
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