Difference between revisions of "Galaxy"

Revision as of 22:05, 12 March 2011 (view source) Olen@acm.org (Talk) (→‎Get datasets for our genome) ← Older edit		Revision as of 04:12, 29 March 2011 (view source) Clements (Talk | contribs) m Newer edit →
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−	{{SessionHead}}	+	{{ImageCenter|GalaxyLogoBigger.png|Galaxy||http://getgalaxy.org/}}
−	{| class="tutorialheader"	+	__NOTITLE__
−	| {{TutorialTitleLine|[[gmod:Galaxy|Galaxy]]}}<br />	+
−	[[2011 GMOD Spring Training]]<br />	+
−	8-12 March 2011<br />	+
−	[[User:Clements|Dave Clements]] and James Taylor (''in absentia'')	+
−	| align="right" | [[Image:GMODAmericas2011Logo.png|200px]]	+
−	|}	+
		+	{{ComponentBox|{{GalaxyResourcesBoxItem}}|{{ComponentBoxEventsHeader}}||{{BioITWorldBoxItem}}|<hr />{{GCCBoxItem}}<hr />{{ESHGBoxItem}}|<hr />{{AGSBoxItem}}<hr />{{WCGBoxItem}}<hr />{{ISMBBoxItem}}}}
		+	[http://usegalaxy.org Galaxy] is an open, web-based platform for ''accessible, reproducible, and transparent'' computational biomedical research.
		+	* ''Accessibility:'' Galaxy enables users without programming experience to easily specify parameters and run tools and workflows.
		+	* ''Reproducibility:'' Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis.
		+	* ''Transparency:'' Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis.
−	[http://galaxyproject.org Galaxy] is a framework for integrating computational tools. It allows nearly any tool that can be run from the command line to be wrapped in a structured well defined interface.	+	Galaxy is open source for all organizations. The [http://usegalaxy.org public Galaxy service] makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by [http://getgalaxy.org downloading the Galaxy application] and customizing it to meet particular needs.
−	On top of these tools, Galaxy provides an accessible environment for interactive analysis that transparently tracks the details of analyses, a workflow system for convenient reuse, data management, sharing, publishing, and more.	+	== 2011 Galaxy Community Conference ==
−	= Creating a Galaxy instance =	+	{{ImageLeft|GCC2011Logo.png|2011 Galaxy Community Conference|300|http://galaxy.psu.edu/gcc2011/}}
		+	The [http://galaxy.psu.edu/gcc2011/ 2011 Galaxy Community Conference] will be held 25-26 May, at the Conference Centre De Werelt in Lunteren, The Netherlands. This year the conference is co-organized by the [http://www.nbic.nl/ Netherlands Bioinformatics Centre (NBIC)].  The conference features [http://galaxy.psu.edu/gcc2011/Programme.html 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 research. If you have or intend to deploy Galaxy, or if you are a tool developer or a data provider then you are strongly encouraged to attend.
−	== Getting Galaxy ==	+	=== Deadlines ===
−		+	{| class="wikitable"
−	=== Prerequisites ===	+	| February 28
−		+	| [http://galaxy.psu.edu/gcc2011/Abstracts.html Abstract Submission] Deadline
−	The only prerequisite to run your own Galaxy is a Python interpreter, version 2.4 or greater. Python 3 is a different language and is currently not supported. The Ubuntu VM images used for this course include version 2.6.4 of the interpreter:	+	|-
−		+	| April 24
−	gmod@ubuntu:~$ <span class="enter">python --version</span>	+	| [http://galaxy.psu.edu/gcc2011/Register.html Early Registration] Deadline
−	Python 2.6.4	+	|}
−		+
−	Galaxy is distributed (and developed) using a distributed version control system called [http://mercurial.selenic.com/ Mercurial]. The Ubuntu VM image already includes mercurial version 1.3.1:	+
−		+
−	gmod@ubuntu:~$ <span class="enter">hg --version</span>	+
−	Mercurial Distributed SCM (version 1.3.1)	+
−	...	+
−		+
−	=== Cloning the Galaxy repository ===	+
−		+
−	The development and release repositories are available through the [http://bitbucket.org bitbucket hosting service].	+
−		+
−	<div class="dont">	+
−	'''DO NOT DO THIS NOW''': To create a local clone of the release repository run the following:	+
−	<pre class="dont">	+
−	gmod@ubuntu:~$ cd ~/work	+
−	gmod@ubuntu:~/work$ hg clone http://bitbucket.org/galaxy/galaxy-dist	+
−	</pre>	+
−	</div>	+
−	'''DO THIS INSTEAD''': To ensure we are all using the exact same revision of Galaxy, instead clone from a repository that is already on the VM image:	+
−		+
−	gmod@ubuntu:~$ <span class="enter">cd ~/work</span>	+
−	gmod@ubuntu:~/work$ <span class="enter">hg clone ~/Documents/Software/galaxy/galaxy-dist</span>	+
−		+
−	Either is equivalent, and the resulting repository can later be updated from any other Galaxy clone.	+
−		+
−	= Initial Setup and Run =	+
−		+
−	== Set the port ==	+
−		+
−	Often you can just fire up Galaxy at this point.  However, if you are following this tutorial using a [[VMware]] image from the [[2011 GMOD Spring Training]] course, this may not work.  The issue is that Galaxy, like [[InterMine]] (also covered at that course), will by default listen to port 8080.  InterMine is already using port 8080 on the course image.  Therefore, to avoid a collision with InterMine, let's do InterMine one better and use port 8081.	+
−		+
−	gmod@ubuntu:~/work$ <span class="enter">cd ~/work/galaxy-dist</span>	+
−		+
−	Galaxy's main configuration file, <tt>universe_wsgi.ini</tt>, sets the port.  By default, that file is created at initialization time by copying <tt>universe_wsgi.ini.sample</tt>.  However, if the file already exists, it will use the already existing file.	+
−		+
−	$ <span class="enter">cp universe_wsgi.ini.sample universe_wsgi.ini</span>	+
−	$ <span class="enter">gedit universe_wsgi.ini</span>	+
−		+
−	Change this:	+
−		+
−	#port = 8080	+
−		+
−	to this:	+
−		+
−	<span class="enter">port = 8081</span>	+
−		+
−	and save the file.	+
−		+
−	== Run Galaxy! Run! ==	+
−		+
−	Galaxy includes a script to run it.  This script also does the initialization of Galaxy, the first time it is run.  Run it now:	+
−		+
−	gmod@ubuntu:~/work/galaxy-dist$ <span class="enter">sh run.sh</span>	+
−	Initializing external_service_types_conf.xml from external_service_types_conf.xml.sample	+
−	Initializing datatypes_conf.xml from datatypes_conf.xml.sample	+
−	Initializing reports_wsgi.ini from reports_wsgi.ini.sample	+
−	Initializing tool_conf.xml from tool_conf.xml.sample	+
−	... (a minute or two or three will pass) ...	+
−	galaxy.web.buildapp DEBUG 2011-02-25 13:01:32,295 Enabling 'x-forwarded-host' middleware	+
−	Starting server in PID 5153.	+
−	serving on http://127.0.0.1:8081	+
−		+
−	This script performs several significant actions the first time it is run:	+
−		+
−	* Creates initial configuration files, including the main file <tt>universe_wsgi.ini</tt> (but not this time, because we created it), and empty directories for storing data files	+
−	* Fetches all of the Galaxy framework's [http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs dependencies], packaged as Python eggs, for the current platform.	+
−	* Initialize its database. Galaxy uses a database migration system to automatically handle any changes to the database schema. On first load it runs all migrations to ensure the database is in a known state, which may take a little time.	+
−		+
−	<!--	+
−	<div class="dont">	+
−	'''Don't do this unless there are problems with the above''': We have also included a local copy of the eggs on the VM image, so if there are any problems fetching the eggs, just type:	+
−	<pre class="dont">	+
−	gmod@ubuntu:~/work/galaxy-dist$ cp -R /home/gmod/Documents/Software/galaxy/eggs-py2.6-linux-i686-ucs4/ eggs/	+
−	</pre>	+
−	</div>	+
−	-->	+
−	Once the database is initialized, the normal startup process proceeds, loading tool configurations, starting the job runner, and finally initializing the web interface on port. You can now access your Galaxy at http://localhost:8081	+
−		+
−	See [http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy GetGalaxy] for more information on setting up Galaxy on other platforms (e.g. Mac OS X).	+
−		+
−	= Running analyses with Galaxy =	+
−		+
−	Without any additional configuration, there is already a lot we can do with our first Galaxy instance. As an example, let's work through the first example from our recent [http://lava.mathcs.emory.edu/outgoing/publications/galaxy_cpmb_2010.pdf Current Protocols in Molecular Biology publication].	+
−		+
−	=== 1. Access your new Galaxy instance ===	+
−		+
−	Load a web browser and access http://localhost:8081.	+
−		+
−	[[Image:Galaxy_FirstAnalysis_1.png]]	+
−		+
−	=== 2. Upload TAF1 ChIP-Seq data ===	+
−		+
−	To use data in an analysis in Galaxy, it first needs to be imported into the current history. There are many ways to do this, but the simplest is by uploading or fetching a file.	+
−		+
−	In the '''Tools''' panel ''select'' '''Get Data''' &rarr; '''Upload File'''. You can either upload a file, or enter one or more URLs in the '''URL/Text''' box. ''Enter''	+
−		+
−	<span class="enter">ftp://ftp.gmod.org/pub/gmod/Courses/2011/SpringTraining/Galaxy/TAF1_ChIP.txt</span>	+
−	:<div style="font-size: 80%">('''Note:''' You can also upload this from the filesystem at <tt>~/Documents/Data/galaxy/)</tt></div>	+
−	in the '''URL/Text''' box and ''click'' '''Execute'''.	+
−		+
−	Galaxy will run the upload tool. Because we are fetching data from an external URL, the job will run in the background. It will first appear in the history as queued (gray), then running (yellow) and finally done (green). At this point, ''clicking'' on the '''name of the dataset in the history''' will show you information about the uploaded file, including the first few lines.	+
−		+
−	[[Image:Galaxy_FirstAnalysis_2.png]]	+
−		+
−	=== 3. Edit Dataset Attributes ===	+
−		+
−	The dataset we uploaded is a generic tabular data file (dumped out of the UCSC browser, not in any particular feature format like BED or [[GFF]]). However, it is feature data, meaning that each row represents a location on a genome. To let Galaxy know about this, ''click'' the '''pencil icon''' in the dataset's '''History''' entry to show the dataset attributes interface. Under '''Change data type''' ''set'' '''New Type:''' to '''interval''' and then ''click'' '''Save'''.	+
−		+
−	Galaxy will look at the dataset and guess which columns represent chromosome, start, end, ''et cetera''. In this case it guesses correctly.	+
−		+
−	We also need to tell Galaxy what genome assembly the intervals correspond to. ''Click'' the dataset's '''pencil icon''' again, and then under '''Database / Build:''' ''select'' '''Human Mar. 2006 (NCBI36/hg18) (hg18)'''. Then ''click'' '''Save'''.	+
−		+
−	[[Image:Galaxy_FirstAnalysis_3.png]]	+
−		+
−	=== 4. Get Gene Annotations from UCSC ===	+
−		+
−	Another major way to pull data into Galaxy is through interfaces with external data providers. Several of these are pre-configured out of the box, including interfaces to [[InterMine]], [[gmod:BioMart|BioMart]] and the UCSC Table Browser. Here we will pull gene annotations from UCSC.	+
−		+
−	In the '''Tools''' panel, ''select'' '''Get Data''' &rarr; '''UCSC Main Table Browser'''. The Table Browser UI will load in the center panel.  Because the data is of human annotations, make sure that '''Clade, Genome''', and '''Assembly''' are ''set'' to '''Mammal, Human''', and '''Mar. 2006''', respectively. ''Set'' '''Group''' to '''Genes and Gene Prediction Tracks''' and '''Track''' to '''RefSeq Genes'''. ''Set'' the '''region''' to '''Genome'''. Make sure '''Output Format''' is ''set'' to '''BED - Browser Extensible Data''' and the check-box by '''Send Output to Galaxy''' is '''checked'''. Finally, ''click'' '''get output'''.	+
−		+
−	[[Image:Galaxy_FirstAnalysis_4.png]]	+
−		+
−	A second interface will load allowing you to specify what portion of genes to select, make sure '''Whole Gene''' is ''selected'' and ''click'' '''Send query to Galaxy'''.	+
−		+
−	[[Image:Galaxy_FirstAnalysis_4-5.png]]	+
−		+
−	=== 5. Generate a set of putative promoter regions ===	+
−		+
−	You should now have two datasets in your history. Dataset 1 containing TAF ChIP-seq intervals, and Dataset 2 containing RefSeq gene annotations. We will now use a Galaxy tool to (naively) create a set of putative promoter regions.	+
−		+
−	In the '''Tools''' panel, ''select'' '''Operate on Genomic Intervals''' &rarr; '''Get Flanks'''. The user interface for the tool will appear in the center panel. Make sure the dataset '''2: UCSC Main...''' is ''selected'' and ''set'' '''Length of Flanking region''' to '''1000''' to create intervals 1000bp upstream of each gene.  ''Click'' '''Execute'''.	+
−		+
−	[[Image:Galaxy_FirstAnalysis_5.png]]	+
−		+
−	=== 6. Identify promoter regions containing TAF1 sites ===	+
−		+
−	Finally, we will join this dataset with our original TAF1 dataset to select promoter regions with TAF1 sites. In the '''Tools''' sections ''select'' '''Operate on Genomic Intervals &rarr; Join''' and ''select'' '''3: Get Flanks...''' as the first dataset and '''1: <nowiki>ftp://ftp.gmod...</nowiki>''' as the second dataset. ''Click'' '''Execute'''.	+
−		+
−	[[Image:Galaxy_FirstAnalysis_6.png]]	+
−		+
−	The resulting dataset will contain all promoter regions that contain a TAF1 site, joined side-by-side with the TAF1 sites they contain. From here we can process further or visualize at different browsers.	+
−		+
−	= Under the hood =	+
−		+
−	Now that we've run some analyses, let's look at how Galaxy is organized and how it handles our data. Return to the terminal, and ''hit'' '''Control-C''' to terminate the Galaxy instance.	+
−		+
−	== Data and metadata ==	+
−		+
−	Within our Galaxy instance directory, instance data is stored under the <tt>database</tt> directory:	+
−		+
−	gmod@ubuntu:~/work/galaxy-dist$ <span class="enter">ls database/</span>	+
−	compiled_templates  info.txt              pbs  universe.sqlite	+
−	files              job_working_directory  tmp  whoosh_indexes	+
−		+
−	Two key files are <tt>universe.sqlite</tt> which is a {{GlossaryLink|Relational|relational database}} containing all the metadata tracked by Galaxy, and the <tt>files</tt> directory which contains the raw datasets. First let's look at the database using the SQLite command line interface:	+
−		+
−	gmod@ubuntu:~/work/galaxy-dist$ <span class="enter">sqlite3 database/universe.sqlite</span>	+
−	SQLite version 3.6.16	+
−	Enter ".help" for instructions	+
−	Enter SQL statements terminated with a ";"	+
−	sqlite>	+
−		+
−	For example, let's look at the first dataset we created:	+
−		+
−	sqlite> <span class="enter">select * from history_dataset_association limit 1;</span>	+
−	1|1|1|2011-02-25 23:10:08.399957|2011-02-25 23:33:22.081694||1|ftp://ftp.gmod.org/pub/gmod/Courses/2011/SpringTraining/Galaxy/TAF1_ChIP.txt|uploaded tabular file|200 regions|#bin chrom chromStart chromEnd name score floatScore	+
−	1470 chr7 116099071 116100373 26384 720 2.183	+
−	1589 chr5 131622266 131623568 26442 679 2.06	+
−	1590 chr5 131854028 131855330 26415 693 2.102	+
−	1591 chr5 131859918 131861220 26451 675 2.048	+
−	1592 chr5 132109996 132111298 26337 764 2.317	+
−	|tabular|{"column_types": ["int", "str", "int", "int", "int", "int", "float"], "columns": 7, "comment_lines": 1, "data_lines": 200, "dbkey": "hg18"}|||0|1|	+
−		+
−	We see that this table tracks all the information the Galaxy interface needs to work with this dataset, include user defined fields such as name and info, as well as the first few lines of the dataset ("peek"), and the type specific metadata.	+
−		+
−	Exit the sqlite interface by ''pressing'' '''Control-D'''.	+
−		+
−	Now let's look at the actual data.	+
−		+
−	gmod@ubuntu:~/work/galaxy-dist$ <span class="enter">find database/files/</span>	+
−	database/files	+
−	database/files/000	+
−	database/files/000/dataset_1.dat	+
−	database/files/000/dataset_2.dat	+
−	database/files/000/dataset_3.dat	+
−	database/files/000/dataset_4.dat	+
−		+
−	All of the datasets corresponding to our history items are stored in this directory. Datasets are broken up into a hierarchy based on ID to avoid problems with particular filesystems. If we look at a single file:	+
−		+
−	gmod@ubuntu:~/work/galaxy-dist$ <span class="enter">head database/files/000/dataset_1.dat</span>	+
−	#bin chrom chromStart chromEnd name score floatScore	+
−	1470 chr7 116099071 116100373 26384 720 2.183	+
−	1589 chr5 131622266 131623568 26442 679 2.06	+
−	1590 chr5 131854028 131855330 26415 693 2.102	+
−	1591 chr5 131859918 131861220 26451 675 2.048	+
−	1592 chr5 132109996 132111298 26337 764 2.317	+
−	1593 chr5 132140320 132141622 26374 729 2.21	+
−	1471 chr11 116212868 116214170 26386 718 2.178	+
−	816 chr22 30341490 30342792 26387 718 2.176	+
−	102 chr22 30670342 30671644 26475 663 2.01	+
−		+
−	we see that Galaxy just stores the raw data exactly as we uploaded it.	+
−		+
−	== Tools ==	+
−		+
−	Galaxy reads all of its tool configuration from a series of {{GlossaryLink|XML|XML}} files. The file <tt>tool_conf.xml</tt> defines which tools are loaded by a given instance:	+
−		+
−	gmod@ubuntu:~/work/galaxy-dist$ <span class="enter">head tool_conf.xml</span>	+
−	<xml> <?xml version="1.0"?>	+
−	<toolbox>	+
−	<section name="Get Data" id="getext">	+
−	<tool file="data_source/upload.xml"/>	+
−	<tool file="data_source/ucsc_tablebrowser.xml" />	+
−	<tool file="data_source/ucsc_tablebrowser_test.xml" />	+
−	<tool file="data_source/ucsc_tablebrowser_archaea.xml" />	+
−	<tool file="data_source/bx_browser.xml" />	+
−	<tool file="data_source/microbial_import.xml" />	+
−	<tool file="data_source/biomart.xml" /></xml>	+
−		+
−	Each referenced file contains the description of a particular tool. The '''Get Flanks''' tool we used earlier is described farther down:	+
−		+
−	<xml>  <section name="Operate on Genomic Intervals" id="bxops">	+
−	<tool file="new_operations/intersect.xml" />	+
−	...	+
−	<tool file="new_operations/join.xml" />	+
−	<tool file="new_operations/get_flanks.xml" />	+
−	<tool file="new_operations/flanking_features.xml" />	+
−	<tool file="annotation_profiler/annotation_profiler.xml" />	+
−	</section></xml>	+
−		+
−	Let's examine the '''Get Flanks''' tool by looking at the file <tt>tools/new_operations/get_flanks.xml</tt>:	+
−	<xml><tool id="get_flanks1" name="Get flanks">	+
−	<description>returns flanking region/s for every gene</description>	+
−	<command interpreter="python">get_flanks.py $input $out_file1 $size $direction $region -o $offset \	+
−	-l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command>	+
−	<inputs>	+
−	<param format="interval" name="input" type="data" label="Select data"/>	+
−	<param name="region" type="select" label="Region">	+
−	<option value="whole" selected="true">Whole feature</option>	+
−	<option value="start">Around Start</option>	+
−	<option value="end">Around End</option>	+
−	</param>	+
−	<param name="direction" type="select" label="Location of the flanking region/s">	+
−	<option value="Upstream">Upstream</option>	+
−	<option value="Downstream">Downstream</option>	+
−	<option value="Both">Both</option>	+
−	</param>	+
−	<param name="offset" size="10" type="integer" value="0" label="Offset"	+
−	help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/>	+
−	<param name="size" size="10" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>	+
−	</inputs>	+
−	<outputs>	+
−	<data format="interval" name="out_file1" metadata_source="input"/>	+
−	</outputs>	+
−	<tests>	+
−	...	+
−	</tests>	+
−	<help>	+
−	...	+
−	</help>	+
−	</tool></xml>	+
−		+
−	This syntax is defined at [https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Tool Config Syntax] on the Galaxy wiki.  You can guess what most of it is about, but some of it, such as:	+
−	${input.metadata.chromCol}	+
−		+
−	is less clear.  A set of ''metadata information'' is defined for each supported data type.  In this case, the input is defined as format <tt>interval</tt>.  Known formats are defined in the data types classes in <tt>lib/galaxy/datatypes/</tt>.  Let's look at  <tt>lib/galaxy/datatypes/interval.py</tt>, which defines interval formats.  To find each type's metadata elements, search for <tt>MetadataElement</tt>:	+
−		+
−	<python>class Interval( Tabular ):	+
−	"""Tab delimited data containing interval information"""	+
−	file_ext = "interval"	+
−		+
−	"""Add metadata elements"""	+
−	MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )	+
−	MetadataElement( name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter )	+
−	MetadataElement( name="endCol", default=3, desc="End column", param=metadata.ColumnParameter )	+
−	MetadataElement( name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 )	+
−	MetadataElement( name="nameCol", desc="Name/Identifier column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 )	+
−	MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False )</python>	+
−		+
−	Test and help details have been removed from the listing here.  The <tt><help></tt> section describes the tool.  This text is displayed on the tool page.  The markup used is [http://docutils.sourceforge.net/docs/user/rst/quickref.html reStructured Text (RST)], a popular markup language in the Python community.	+
−		+
−	This file contains everything necessary to define the user interface of the tool. Compare the inputs element with the figure of the '''Get Flanks''' tool interface above.	+
−		+
−	It also describes how to take a set of user input values from the generated user interface, and construct a command line to actually run the tool. Nearly all tools in Galaxy are constructed in this way -- any analysis that can be run from the command line can be integrated into a Galaxy instance.	+
−		+
−	= Configuring Galaxy (2) =	+
−		+
−	== Using a more robust database ==	+
−		+
−	Out of the box Galaxy includes the embedded SQLite database. This allows Galaxy to run with zero-configuration and provides an excellent solution for single-user Galaxy's being used for tool development. However, for any multi-user scenario a more robust database will be needed for Galaxy to be reliable. We '''highly''' recommend [[gmod:PostgreSQL|Postgres]], although other database are known to work.	+
−		+
−	Postgres is already installed on our [[VMware Setup|VM image]] (it's the default {{GlossaryLink|DBMS|DBMS}} for [[Chado]]), and the <tt>gmod</tt> user has permission to create databases, so let's create a database for Galaxy	+
−		+
−	gmod@ubuntu:~/work/galaxy-dist$ <span class="enter">createdb galaxy_test</span>	+
−		+
−	Once the empty database is created, we need to edit Galaxy's <tt>universe_wsgi.ini</tt> file to use it:	+
−	# Setting <tt>database_connection</tt> to <tt>postgres://gmod:gmodamericas2011@localhost:5432/galaxy_test</tt>.	+
−	# Setting <tt>database_engine_option_server_side_cursors</tt> to <tt>True</tt>	+
−	# Setting <tt>database_engine_option_strategy</tt> to <tt>threadlocal</tt>	+
−	With these changes the <tt>Database</tt> section of your Galaxy config file will look like:	+
−		+
−	# -- Database	+
−		+
−	# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'.  You	+
−	# may use a SQLAlchemy connection string to specify an external database	+
−	# instead.  This string takes many options which are explained in detail in the	+
−	# config file documentation.	+
−	#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE	+
−	<span class="enter">database_connection = postgres://gmod:gmodamericas2011@localhost:5432/galaxy_test</span>	+
−		+
−	# If the server logs errors about not having enough database pool connections,	+
−	# you will want to increase these values, or consider running more Galaxy	+
−	# processes.	+
−	#database_engine_option_pool_size = 5	+
−	#database_engine_option_max_overflow = 10	+
−		+
−	# If using MySQL and the server logs the error "MySQL server has gone away",	+
−	# you will want to set this to some positive value (7200 should work).	+
−	#database_engine_option_pool_recycle = -1	+
−		+
−	# If large database query results are causing memory or response time issues in	+
−	# the Galaxy process, leave the result on the server instead.  This option is	+
−	# only available for PostgreSQL and is highly recommended.	+
−	<span class="enter">database_engine_option_server_side_cursors = True</span>	+
−		+
−	# Create only one connection to the database per thread, to reduce the	+
−	# connection overhead.  Recommended when not using SQLite:	+
−	<span class="enter">database_engine_option_strategy = threadlocal</span>	+
−		+
−	# Log all database transactions, can be useful for debugging and performance	+
−	# profiling.  Logging is done via Python's 'logging' module under the qualname	+
−	# 'galaxy.model.orm.logging_connection_proxy'	+
−	#database_query_profiling_proxy = False	+
−		+
−	== Tool dependencies ==	+
−		+
−	So far we have used tools that are completely packaged with the Galaxy distribution. However, many tools require external software to be installed to be used (we are currently working on an enhanced dependency management system to make this easier). In the meantime, we maintain a list of [http://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies tool dependencies]. Suppose we'd like to analyze some Illumina datasets. We see that the '''Map with BWA''' tool requires us to install [http://bio-bwa.sourceforge.net/ BWA] (surprise!). To save time, BWA is already compiled on the [[VMware Setup|VM image]], so let's copy it to a location on the <tt>PATH</tt>:	+
−		+
−	$ <span class="enter">sudo cp /home/gmod/Documents/Software/galaxy/bwa-0.5.9/bwa /usr/local/bin</span>	+
−		+
−	Now <tt>bwa</tt> can be run from the command line:	+
−		+
−	$ <span class="enter">bwa</span>	+
−		+
−	Program: bwa (alignment via Burrows-Wheeler transformation)	+
−	Version: 0.5.9-r16	+
−	Contact: Heng Li <lh3@sanger.ac.uk>	+
−		+
−	...	+
−		+
−	The Galaxy tool also requires a <tt>loc</tt> file which contains the locations of indexes for locally stored genome builds. We don't have any, so we can just use the empty sample:	+
−		+
−	$ <span class="enter">cp tool-data/bwa_index.loc.sample tool-data/bwa_index.loc</span>	+
−		+
−	and run Galaxy using <tt>sh run.sh</tt>	+
−		+
−	= A second example with NGS data =	+
−		+
−	Having made these changes, start Galaxy again using <tt>run.sh</tt> and access it at	+
−	http://localhost:8081	+
−		+
−	<!--	+
−	And the <tt> sh ./run.sh</tt> fails.  Type this magic:	+
−	<pre class="enter"> sudo ln -s /var/run/postgresql/.s.PGSQL.5432 /tmp/	+
−	sh ./run.sh</pre>	+
−		+
−	We don't know why.	+
−	-->	+
−		+
−	You will notice that your history has been lost. This is the result of moving to Postgres. On startup, Galaxy will again have created a new database from scratch.	+
−		+
−	=== 1. Upload datasets ===	+
−		+
−	We will again use the '''Get Data &rarr; Upload File''' tool to upload data into Galaxy. You can enter multiple URLs into the '''URL / Text''' box. ''Enter:''	+
−		+
−	<pre>	+
−	ftp://ftp.gmod.org/pub/gmod/Courses/2011/SpringTraining/Galaxy/phiX174_genome.fa	+
−	ftp://ftp.gmod.org/pub/gmod/Courses/2011/SpringTraining/Galaxy/phiX174_reads.fastqsanger	+
−	</pre>	+
−	and ''click'' '''Execute''':	+
−		+
−	[[Image:Galaxy_SecondAnalysis_1.png]]	+
−		+
−	After uploading the datasets, ''expand them'' in the '''History'''. We can see that Galaxy has successfully detected the file formats of both files.	+
−		+
−	[[Image:Galaxy_SecondAnalysis_2.png]]	+
−		+
−	However, we need to make one modification. The FASTQ format is ill-defined, and Galaxy needs to know how the quality scores are scaled. ''Click'' the '''pencil icon for dataset 2''', and ''change'' the '''datatype''' from '''fastq''' to '''fastqsanger''' (be careful, there are many similar choices here). Finally, ''click'' '''Save'''.	+
−		+
−	== 2. Run BWA to map reads ==	+
−		+
−	In the '''Tools''' panel, ''select'' '''NGS: Mapping &rarr; Map with BWA for Illumina'''.	+
−		+
−	''Change'' the value of the first parameter to '''Use one from the history''' and make sure that '''1: http://...genome.fa''' is '''selected'''.	+
−		+
−	Make sure that for parameter '''FASTQ file''' that '''2: http://...fastqsanger''' is selected.	+
−		+
−	''Click'' '''Execute'''.	+
−		+
−	A new dataset is generated containing the mapped reads in {{GlossaryLink|SAM|SAM format}}.	+
−		+
−	[[Image:Galaxy_SecondAnalysis_3.png]]	+
−		+
−	= Adding a new tool =	+
−		+
−	The [http://samtools.sourceforge.net/ SAM format] contains 12 required fields representing the read and the position it maps to, followed by a variable number of optional fields of the form <tt>''CODE:TYPE:VALUE''</tt>. Suppose we want to filter by these optional fields. We can whip up a quick command line tool in Python (or perl, or awk, or...) to do this.	+
−		+
−	Let's first create a directory for our new tool:	+
−		+
−	gmod@ubuntu:~/work/galaxy-dist$ <span class="enter">mkdir tools/gmod_2011</span>	+
−		+
−	== The tool command (script) ==	+
−		+
−	And then using a [[Linux Text Editors|text editor]], create <tt>tools/gmod_2011/sam_filter.py</tt> containing:	+
−		+
−	<python>#!/usr/bin/env python	+
−		+
−	"""	+
−	Usage: sam_filter.py input_file output_file flag value	+
−	"""	+
−		+
−	import sys	+
−		+
−	out = open( sys.argv[2], "w" )	+
−		+
−	for line in open( sys.argv[1] ):	+
−	# Strip end of line and split on tabs	+
−	fields = line.rstrip( "\r\n" ).split( "\t" )	+
−	# Look only at optional fields	+
−	write_line = False	+
−	for field in fields[12:]:	+
−	flag, type, value = field.split( ":" )	+
−	if flag == sys.argv[3] and value == sys.argv[4]:	+
−	write_line = True	+
−	# If any optional field matched, keep the read	+
−	if write_line:	+
−	out.write( line )</python>	+
−		+
−	== The tool wrapper ==	+
−		+
−	Next, we need to create the tool configuration. Edit the file <tt>tools/gmod_2011/sam_filter.xml</tt> and start with the following skeleton:	+
−		+
−	<xml><tool id="sam_filter_1" name="SAM Filter">	+
−	<command interpreter="python">	+
−		+
−	</command>	+
−	<inputs>	+
−		+
−	</inputs>	+
−	<outputs>	+
−		+
−	</outputs>	+
−	</tool></xml>	+
−		+
−	First, let's define the output. This tool has a single output, of type <tt>sam</tt>, so we modify the configuration to contain:	+
−		+
−	<xml><tool id="sam_filter_1" name="SAM Filter">	+
−	<command interpreter="python">	+
−		+
−	</command>	+
−	<inputs>	+
−		+
−	</inputs>	+
−	<outputs>	+
−	<data name="output1" format="sam" />	+
−	</outputs>	+
−	</tool></xml>	+
−		+
−	The name can be anything, but it will be used later to identify the output file in the command line. Second, let's define the following inputs	+
−		+
−	* An input dataset of type <tt>sam</tt>	+
−	* An input flag, which is selected from a predefined set	+
−	* An input value, which can be any text	+
−		+
−	The resulting configuration:	+
−		+
−	<xml><tool id="sam_filter_1" name="SAM Filter">	+
−	<command interpreter="python">	+
−		+
−	</command>	+
−	<inputs>	+
−	<param type="data" format="sam" name="input1" label="File to filter"/>	+
−	<param type="select" name="flag" label="Optional field to filter on">	+
−	<option value="NM">Edit Distance</option>	+
−	<option value="MD">Mismatching positions / bases</option>	+
−	<option value="AS">Alignment score</option>	+
−	</param>	+
−	<param type="text" name="value" label="Value to require for flag"/>	+
−	</inputs>	+
−	<outputs>	+
−	<data name="output1" format="sam" />	+
−	</outputs>	+
−	</tool></xml>	+
−		+
−	Finally, we define how to construct our command line based on values for the inputs. The command line is a template, where we can substitute in the value of each input (filenames in the case of datasets). Thus our final tool configuration is:	+
−		+
−	<xml><tool id="sam_filter_1" name="SAM Filter">	+
−	<command interpreter="python">	+
−	sam_filter.py $input1 $output1 $flag $value	+
−	</command>	+
−	<inputs>	+
−	<param type="data" format="sam" name="input1" label="File to filter"/>	+
−	<param type="select" name="flag" label="Optional field to filter on">	+
−	<option value="NM">Edit Distance</option>	+
−	<option value="MD">Mismatching positions / bases</option>	+
−	<option value="AS">Alignment score</option>	+
−	</param>	+
−	<param type="text" name="value" label="Value to require for flag"/>	+
−	</inputs>	+
−	<outputs>	+
−	<data name="output1" format="sam" />	+
−	</outputs>	+
−	</tool></xml>	+
−		+
−	We now need to modify <tt>tool_conf.xml</tt> to register our new tool and run Galaxy. Modify the top of <tt>tool_conf.xml</tt> to look like:	+
−		+
−	<xml><?xml version="1.0"?>	+
−	<toolbox>	+
−	<section name="GMOD 2011 Course Tools" id="gmod_2011">	+
−	<tool file="gmod_2011/sam_filter.xml"/>	+
−	</section>	+
−	...</xml>	+
−		+
−	and run Galaxy using <tt>run.sh</tt>	+
−		+
−	== Running the new tool ==	+
−		+
−	Return to the Galaxy web interface and from the '''Tools''' panel and ''select'' '''GMOD 2011 Course Tools &rarr; SAM Filter'''.	+
−		+
−	The dataset '''3: Map with BWA...''' should already be '''selected'''. Because we defined the type of data the tool can accept, Galaxy knows this is the only dataset in our history that is valid.	+
−		+
−	''Select'' '''Edit distance''' for the '''flag''', ''enter'' '''0''' for the '''value''', and ''click'' '''Execute'''.	+
−		+
−	[[Image:Galaxy_SamFilter_1.png]]	+
−		+
−	We know have a new dataset '''4: Sam Filter on data 3''' which contains only reads that mapped exactly to the reference.	+
−		+
−	[[Image:Galaxy_SamFilter_2.png]]	+
−		+
−	= Galaxy Workflows =	+
−		+
−	The Galaxy workflow system allows analysis containing multiple tools to be built, run, extracted from histories, and rerun. As a trivial example, let's extract a workflow for the analysis we just performed.	+
−		+
−	We'll first need to create a user account and login. At the top of the Galaxy interface, select '''User &rarr; Register'''. ''Fill in'' the required fields and ''click'' '''Submit'''. Your account will be created, and you will be logged in (retaining your current history).	+
−		+
−	In the title of the '''History''' panel, ''click'' '''Options &rarr; Extract Workflow'''.	+
−		+
−	At this point, you have the option to select a subset of steps from your history to include in the workflow. Some tools cannot be used as workflow steps (e.g. uploads) so they will instead be treated as inputs to the workflow. This is fine, so ''click'' '''Create Workflow'''.	+
−		+
−	[[Image:Galaxy_Misc_1.png]]	+
−		+
−	Now, from the top bar ''click'' '''Workflow''' to see a list of your workflows. You should see one workflow. ''Click'' on '''its name''' to bring up a popup menu, then ''click'' '''Edit''' to open the workflow editor. In the workflow editor, we can modify parameters or add and remove steps. For example, if we ''click'' on '''SAM filter''', we can change edit distance from 0 to 1:	+
−		+
−	[[Image:Galaxy_Misc_2.png]]	+
−		+
−	= Making genome / alignment data available to Galaxy =	+
−		+
−	Galaxy is designed so that a single Galaxy instance can work with many genomes simultaneously. To use certain tools, Galaxy needs to be configured to know where to find data for those genomes. As an example, let's create a new fake genome and configure some data for it.	+
−		+
−	Every genome in Galaxy needs to have an unique identifier (called the build identifier or dbkey). For our example, the identifier will be <tt>a_example_1</tt>.	+
−		+
−	== Python package management tools ==	+
−		+
−	<div class="dont">	+
−	'''DO NOT DO THIS NOW''': This has already been done on the [[VMware Setup|VMware]] image.	+
−		+
−	First, install a few packages that will allow us to index our data. At the terminal, enter:	+
−		+
−	<tt>&nbsp;&nbsp;$ <span class="enter">sudo apt-get install python-dev python-setuptools python-pip</span></tt>	+
−	</div>	+
−		+
−	== bx-python ==	+
−		+
−	<div class="dont">	+
−	'''Do not do this now either.'''  This has already been done on your image.	+
−		+
−	This ''would'' install some support files needed by Python. Next type	+
−		+
−	<tt>&nbsp;&nbsp;$ <span class="enter">sudo pip install bx-python</span></tt>	+
−		+
−	This would install the <tt>bx-python</tt> package, a collection of scripts and Python libraries for working with genomic and comparative genomic data.	+
−	</div>	+
−		+
−	== Get datasets for our genome ==	+
−		+
−	Now, we will download the datasets for our example genome:	+
−		+
−	$ <span class="enter">mkdir tool-data/a_example_1</span>	+
−	$ <span class="enter">cd tool-data/a_example_1</span>	+
−	$ <span class="enter">wget ftp://ftp.gmod.org/pub/gmod/Courses/2011/SpringTraining/Galaxy/a_example_1.maf</span>	+
−	$ <span class="enter">wget ftp://ftp.gmod.org/pub/gmod/Courses/2011/SpringTraining/Galaxy/a_example_1.2bit</span>	+
−	<div style="font-size: 80%">	+
−	::Note: These files are also available on the image in <tt>~/Documents/Data/galaxy/</tt>.</div>	+
−		+
−	Next, we will use the script <tt>maf_build_index.py</tt> (put in <tt>/usr/local/bin/</tt> when <tt>bx-python</tt> was installed) to create a binary index that allows fast selection of alignments from a MAF file:	+
−		+
−	$ <span class="enter">maf_build_index.py a_example_1.maf</span>	+
−	$ <span class="enter">ls</span>	+
−	a_example_1.2bit  a_example_1.maf  a_example_1.maf.index	+
−	$ <span class="enter">cd ~/work/galaxy-dist<span>	+
−		+
−	== Edit configuration files ==	+
−		+
−	We now need to edit several configuration files to inform Galaxy of the existence of our genome, and of these associated datasets.	+
−		+
−	'''NOTE:''' these are TAB separated files, and it is important that the tabs are in the right places. If you have trouble cutting and pasting from the wiki, you can cut and paste from this text file instead:	+
−	ftp://ftp.gmod.org/pub/gmod/Courses/2011/SpringTraining/Galaxy/info.txt	+
−		+
−	Add this line to <tt>tool-data/shared/ucsc/builds.txt</tt>	+
−	<pre class="enter">	+
−	a_example_1 Example genome	+
−	</pre>	+
−		+
−	Add this to <tt>tool-data/alignseq.loc</tt>	+
−	<pre class="enter">	+
−	seq a_example_1 /home/gmod/work/galaxy-dist/tool-data/a_example_1/a_example_1.2bit	+
−	</pre>	+
−		+
−	Add this to <tt>tool-data/maf_index.loc</tt>	+
−	<pre class="enter">	+
−	a_example_1 with 3 other species a_example_1_3way a_example_1 a_example_1,apiMel2,n_vitripennis_20100409,dm3 /home/gmod/work/galaxy-dist/tool-data/a_example_1/a_example_1.maf	+
−	</pre>	+
−		+
−	Now, stop and start your running Galaxy with	+
−	<span class="enter"><Control-C></span>	+
−	$ <span class="enter">sh run.sh</span>	+
−		+
−	== Create dataset using new genome build ==	+
−		+
−	Now let's see if our new data is available in Galaxy. Click '''Get Data &rarr; Upload File'''.	+
−		+
−	Paste the following into the '''URL/Text''' box:	+
−		+
−	<pre>	+
−	scaffold0 450 650	+
−	scaffold0 2000 3000	+
−	</pre>	+
−		+
−	Set the '''File Format''' to '''BED''', make sure '''Convert spaces to tabs''' is '''selected''', and click in the '''Genome:''' box. You should be able to find your genome by typing '''example'''.	+
−		+
−	== Extract sequence corresponding to these intervals ==	+
−		+
−	In the '''Tools''' menu, ''click'' '''Fetch Sequences &rarr; Extract Genomic DNA'''.	+
−		+
−	[[Image:Galaxy_Fetch_1.png]]	+
−		+
−	The tool interface should open in the main panel. The default values are probably fine (make sure the dataset you just created is selected). ''Click'' '''Execute'''. A new dataset will be created containing the DNA for your regions of interest.	+
−		+
−	== Extract multiple alignments corresponding to these intervals ==	+
−		+
−	In the '''Tools''' menu, click '''Fetch Alignments &rarr; Extract MAF Blocks'''.	+
−		+
−	[[Image:Galaxy_Fetch_2.png]]	+
−		+
−	The tool interface will open in the main panel. Again, the defaults should be reasonable, but ''click'' '''Select All''' to do alignments to all other species. ''Click'' '''Execute'''. A new dataset will be created containing alignments corresponding to your intervals of interest.	+
−		+
−	[[Image:Galaxy_Fetch_3.png]]	+
−		+
−	== Other Features ==	+
−		+
−	Terminate Galaxy with <tt>Control-C</tt>. Edit <tt>universe_wsgi.ini</tt> again and in the section <tt>[app:main]</tt> add two lines:	+
−		+
−	<pre>	+
−	# enable_tracks = True	+
−	enable_pages = True	+
−	</pre>	+
−		+
−	Restart Galaxy with <tt>run.sh</tt>	+
−		+
−	<div style="font-size: 80%">	+
−	::Note: if you are running this tutorial after the course, pages may be enabled by default in the most current Galaxy distribution.</div>	+
−		+
−	== Galaxy Pages ==	+
−		+
−	The Galaxy pages feature allows the creation of documents that integrate datasets, histories, and workflows.	+
−		+
−	From the '''User''' menu at the top, select '''Saved Pages''' and then ''click'' '''Add new page'''. ''Enter'' a '''Page Title''' and '''Page Annotation''', and a URL compatible identifier will be generated automatically. ''Click'' '''submit''', and you will return to the list of pages.	+
−		+
−	Click the '''arrow to the right of the page name''', and from the popup menu click '''Edit Content'''.	+
−		+
−	You are now in a WYSIWYG editor where you can write-up your analysis for sharing. As a simple example, click '''Embed Galaxy Object &rarr; Embed History''', and then select the history you have been working with, and ''click'' '''Embed'''.	+
−		+
−	[[Image:Galaxy_Misc_3.png]]	+
−		+
−	Click '''Save''' and '''Close''' to return to the page list, and ''click'' on the '''page's title &rarr; View''' to view it. You will now see your page, with your analysis history embedded. This page can be shared with others, or published publicly. Others can inspect your history, import and work with your analysis.	+
−	Note that our history is still named "Unnamed history", which is mildly irritating, given how spiffy it is. To fix this, ''click'' on the '''Analyze Data''' tab, and then at the top of the '''History''' panel, ''click'' on the text '''Unnamed history''' and enter a meaningful history name, such as "Spiffy History".  ''Hit'' the '''return key'''.
−	Now, if you view the page again, you'll see the history has a name.
−	[[Image:Galaxy_Misc_4.png]]	+	==Demo & Screencasts ==
−	''Spiffy!'' You can return to the History view and annotate your history items by clicking on the '''Note icon'''. These annotations will show up with your embedded history.	+	Try the [http://usegalaxy.org/ public Galaxy server].  You can create a login and save your work, or use it anonymously.   Short [http://main.g2.bx.psu.edu/screencast screencasts] on how to use Galaxy for several example tasks are also available.
−	= Where to go next =	+	==Requirements==
−	We've only scratched the surface of what can be done with Galaxy. Here are some pointers for learning more:	+	* Python version '''2.4''' or higher
		+	* '''Mac OS X''' currently requires Universal "Fat" Python 2.4 (the Python 2.4 build officially supported by Apple) from http://macpython.org/ ([http://pythonmac.org/packages/py24-fat/index.html direct link])
		+	* Galaxy runs fine in most Posix environments.  It is not currently supported on Windows platforms, but necessary Python eggs can be built by those desiring to host it on Windows.
−	* [http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise Jeremy Goecks' RNA-seq Analysis Exercise shared page].	+	==Documentation==
−	* [http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax You can build much more complicated tool configurations ]	+
−	* [http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster Your Galaxy instance can run jobs on a cluster ]	+
−	* [http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer Your Galaxy can be more robust and scalable ]	+
−	* [http://bitbucket.org/galaxy/galaxy-central/wiki/DataIntegration You can make local genomes, alignments, and other data available to Galaxy]	+
−	* [http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications/Tutorial You can customize what external applications are available for displaying datasets ]	+
−	* [http://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes You can customize the datatypes for a Galaxy instance]	+
−	* [http://bitbucket.org/galaxy/galaxy-central/wiki/cloud You can instantiate Galaxy on the Amazon cloud]	+
−	* [http://bitbucket.org/galaxy/galaxy-central/wiki/Home You can find even more at the Galaxy wiki]	+
−	== [http://galaxy.psu.edu/gcc2011/ 2011 Galaxy Community Conference] ==	+	* Most Galaxy documentation is in the [http://g2.trac.bx.psu.edu/wiki Galaxy Wiki].
		+	* [http://www.genome.org/cgi/content/abstract/15/10/1451 Galaxy: A platform for interactive large-scale genome analysis], by Belinda Giardine, Cathy Riemer, Ross C. Hardison, Richard Burhans, Laura Elnitski, Prachi Shah, Yi Zhang, [[User:DanB|Daniel Blankenberg]], Istvan Albert, [[User:JamesTaylor|James Taylor]], Webb Miller, W. James Kent and Anton Nekrutenko, Genome Res. 15:1451-1455, 2005
−	{{ImageCenter|GCC2011Logo.png|2011 Galaxy Community Conference|400|http://galaxy.psu.edu/gcc2011/}}	+	== Mailing Lists ==
−	The '''[http://galaxy.psu.edu/gcc2011/ 2011 Galaxy Community Conference]''' will be held 25-26 May, at the [http://www.congrescentrum.com/accommodations/de_werelt Conference Centre De Werelt] in Lunteren, The Netherlands. The conference is co-organized by the [http://www.nbic.nl/ Netherlands Bioinformatics Centre (NBIC)]. The conference features [http://galaxy.psu.edu/gcc2011/Programme.html 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 research. If you have or intend to deploy Galaxy, or if you are a tool developer or a data provider then you are strongly encouraged to attend.	+	{{MailingListsFor|Galaxy}}
−	= Evaluation =	+	==Downloads==
−	{{Feedback}}	+	Galaxy aims to be a zero configuration entirely self-contained system that provides a lightweight webserver, an embedded database and a multi-threaded job manager. All tools (and their parameters) can be specified via simple XML based configuration files.  Galaxy download and installation information is located [http://g2.trac.bx.psu.edu/wiki/HowToInstall here].
−	{{NextSession|Resources|Resources}}	+	[[Category:Analysis]]
		+	[[Category:Comparative Genomics]]
		+	[[Category:GMOD Components]]
		+	[[Category:Annotation]]
		+	[[Category:Galaxy]]

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Revision as of 04:12, 29 March 2011

__NOTITLE__

Status

• Mature release
• Active development
• Active support

Resources

• Project Home
• Download
• Mailing Lists
• Public Server
• Admin Tutorial
• Galaxy 101
• Wiki
• Screencasts
• 2012 Conf.Template:ComponentBoxEventsHeader
  
  April 12-14

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  May 25-26

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May 28-31

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Arthropod
Genomics
June 9-12

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Workshop on
Comparative Genomics
July 10-23

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July 15-19

Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.

• Accessibility: Galaxy enables users without programming experience to easily specify parameters and run tools and workflows.
• Reproducibility: Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis.
• Transparency: Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis.

Galaxy is open source for all organizations. The public Galaxy service makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by downloading the Galaxy application and customizing it to meet particular needs.

2011 Galaxy Community Conference

The 2011 Galaxy Community Conference will be held 25-26 May, at the Conference Centre De Werelt in Lunteren, The Netherlands. This year the conference is co-organized by the Netherlands Bioinformatics Centre (NBIC). The conference features 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 research. If you have or intend to deploy Galaxy, or if you are a tool developer or a data provider then you are strongly encouraged to attend.

Deadlines

Demo & Screencasts

Try the public Galaxy server. You can create a login and save your work, or use it anonymously. Short screencasts on how to use Galaxy for several example tasks are also available.

Requirements

• Python version 2.4 or higher
• Mac OS X currently requires Universal "Fat" Python 2.4 (the Python 2.4 build officially supported by Apple) from http://macpython.org/ (direct link)
• Galaxy runs fine in most Posix environments. It is not currently supported on Windows platforms, but necessary Python eggs can be built by those desiring to host it on Windows.

Documentation

• Most Galaxy documentation is in the Galaxy Wiki.
• Galaxy: A platform for interactive large-scale genome analysis, by Belinda Giardine, Cathy Riemer, Ross C. Hardison, Richard Burhans, Laura Elnitski, Prachi Shah, Yi Zhang, Daniel Blankenberg, Istvan Albert, James Taylor, Webb Miller, W. James Kent and Anton Nekrutenko, Genome Res. 15:1451-1455, 2005

Mailing Lists

Downloads

Galaxy aims to be a zero configuration entirely self-contained system that provides a lightweight webserver, an embedded database and a multi-threaded job manager. All tools (and their parameters) can be specified via simple XML based configuration files. Galaxy download and installation information is located here.