Difference between revisions of "Galaxy"

From GMOD
Jump to: navigation, search
m (Updating data)
m
 
(12 intermediate revisions by 3 users not shown)
Line 1: Line 1:
<!-- to alter this page, please edit the raw data, which is stored at http://gmod.org/wiki/Galaxy/tool_data -->
 
 
{{ :Galaxy/tool_data | template = Template:ToolDisplay }}
 
 
 
{{Tool data
 
{{Tool data
 
|name=Galaxy
 
|name=Galaxy
|full name=
 
 
|status=mature
 
|status=mature
 
|dev=active
 
|dev=active
 
|support=active
 
|support=active
 
|type=Genome Visualization and Editing, Workflow Management, Tool Integration, Analysis
 
|type=Genome Visualization and Editing, Workflow Management, Tool Integration, Analysis
|platform=web, api
+
|platform=web
|about=[http://usegalaxy.org Galaxy] is an open, web-based platform for ''accessible, reproducible, and transparent'' computational biomedical research.
+
|about=[https://galaxyproject.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.
 
* ''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.
 
* ''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.
 
* ''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 [http://usegalaxy.org public Galaxy server] 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.
+
Galaxy is open source for all organizations and is [https://galaxyproject.org/use/ available on a wide variety of platforms and publicly accessible websites]. Galaxy servers make 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.
  
=== 2014 Galaxy Community Conference ===
 
  
[[File:GCC2014Logo.png|left|250px|link=http://wiki.galaxyproject.org/Events/GCC2014|2014 Galaxy Community Conference]]
+
[[File:GCC2019Logo.png|left|250px|link=https://galaxyproject.org/events/gcc2019/ 2019 Galaxy Community Conference]]
 +
 
 +
=== 2019 Galaxy Community Conference ===
 +
 
 +
The [https://galaxyproject.org/events/gcc2019 2019 Galaxy Community Conference (GCC2019)] will be held 1-6 July, in Freiburg Germany. [https://galaxyproejct.org/gcc2 Galaxy Community Conferences] are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it.  The 2019 conference includes training that offers in-depth topic coverage across several concurrent sessions, and a CollaborationFest.
  
The [http://wiki.galaxyproject.org/Events/GCC2014 2014 Galaxy Community Conference (GCC2013)] will be held June 30 through July 2, at the [http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/ Homewood Campus] of [http://jhu.edu Johns Hopkins University]], in [http://visitors.baltimorecity.gov/ Baltimore, Maryland], United States.
 
  
Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it.  The conference will also includes a ''Training Day'' offering in-depth topic coverage, across several concurrent sessions.  See [http://wiki.galaxyproject.org/Events/GCC201 the GCC2013 web site] for an idea of what happens at a Galaxy Community Conference.  The GCC2013 site includes links to slides and videos for all accepted talks.
 
|release date=2005
 
 
|open source=Yes
 
|open source=Yes
 
|licence=[http://opensource.org/licenses/AFL-3.0 Academic Free License 3.0]
 
|licence=[http://opensource.org/licenses/AFL-3.0 Academic Free License 3.0]
|language=Python, XML
 
 
|input=Roadmaps,Sequences,ab1,affybatch,afg,axt,bam,bcf,bed,bedgraph,bigbed,bigwig,bowtie_base_index,bowtie_color_index,chrint,cisml,csfasta,csv,eland,elandmulti,encodepeak,eset,fasta,fastq,fastqcssanger,fastqillumina,fastqsanger,fastqsolexa,fli,fped,fphe,fqtoc,gatk_dbsnp,gatk_interval,gatk_recal,gatk_report,gatk_tranche,gd_indivs,gd_ped,gd_sap,gd_snp,[[GFF]],[[GFF3]],gtf,interval,lav,ldindep,len,linecount,lped,maf,malist,memexml,nex,nhx,pbed,phyloxml,picard_interval_list,pileup,pphe,qual454,qualillumina,qualsolexa,qualsolid,sam,scf,sff,snpmatrix,snptest,tabular,taxonomy,twobit,txt,vcf,velvet,wig,xml
 
|input=Roadmaps,Sequences,ab1,affybatch,afg,axt,bam,bcf,bed,bedgraph,bigbed,bigwig,bowtie_base_index,bowtie_color_index,chrint,cisml,csfasta,csv,eland,elandmulti,encodepeak,eset,fasta,fastq,fastqcssanger,fastqillumina,fastqsanger,fastqsolexa,fli,fped,fphe,fqtoc,gatk_dbsnp,gatk_interval,gatk_recal,gatk_report,gatk_tranche,gd_indivs,gd_ped,gd_sap,gd_snp,[[GFF]],[[GFF3]],gtf,interval,lav,ldindep,len,linecount,lped,maf,malist,memexml,nex,nhx,pbed,phyloxml,picard_interval_list,pileup,pphe,qual454,qualillumina,qualsolexa,qualsolid,sam,scf,sff,snpmatrix,snptest,tabular,taxonomy,twobit,txt,vcf,velvet,wig,xml
 
|output=zillions!
 
|output=zillions!
 +
|language=Python, XML
 
|audience=public,private
 
|audience=public,private
 +
|release date=2005
 +
|use template=Yes
 
|logo=GalaxyLogoBigger.png
 
|logo=GalaxyLogoBigger.png
 
|screenshot=[[File:Galaxy screenshot-1.png|thumb|none|300px|Galaxy 'Upload file' tool]] [[File:Galaxy screenshot-2.png|thumb|none|300px|Galaxy 'Table Browser' tool]] [[File:Galaxy screenshot-3.png|thumb|none|300px|Editing the attributes of a data set in Galaxy]]
 
|screenshot=[[File:Galaxy screenshot-1.png|thumb|none|300px|Galaxy 'Upload file' tool]] [[File:Galaxy screenshot-2.png|thumb|none|300px|Galaxy 'Table Browser' tool]] [[File:Galaxy screenshot-3.png|thumb|none|300px|Editing the attributes of a data set in Galaxy]]
|survey link=Galaxy
 
 
|mail={{MailingListsFor|Galaxy}}
 
|mail={{MailingListsFor|Galaxy}}
|contact email=[mailto:clements@galaxyproject.org Dave Clements] or [mailto:outreach@galaxyproject.org Galaxy Outreach]
+
|papers=See [https://galaxyproject.org/citing-galaxy Citing Galaxy] for a core list of 25+ papers on Galaxy, and the [https://www.zotero.org/groups/1732893/galaxy Galaxy publication library] for a fuller list of papers mentioning or using Galaxy.
|papers=See [http://wiki.galaxyproject.org/CitingGalaxy Citing Galaxy] for a core list of 25+ papers on Galaxy, and the [http://www.citeulike.org/group/16008/ Galaxy CiteULike group] for a fuller list of papers mentioning or using Galaxy.
+
|tutorials=;
|presentations=
+
:A wealth of community created and maintained training materials are available:
|tutorials=;[[Galaxy Tutorial]]
+
:*[https://training.galaxyproject.org Galaxy Training website]
:As taught at the [[2013 GMOD Summer School]]
+
;[http://wiki.galaxyproject.org/Learn Galaxy Learning Hub]:
+
:A wealth of training materials, including:
+
:*[http://wiki.galaxyproject.org/Learn#Galaxy_101 Galaxy 101]
+
:*[http://wiki.galaxyproject.org/Learn/Screencasts Screencasts]
+
:*[http://wiki.galaxyproject.org/Learn#Shared_Pages.2C_Histories_.26_Workflows Shared Pages, Histories & Workflows]
+
:*[http://wiki.galaxyproject.org/Learn#Other_Tutorials Other Tutorials]
+
:*[http://wiki.galaxyproject.org/Learn#Datasets Working With Datasets]
+
:*[http://wiki.galaxyproject.org/Learn and more!]
+
; [http://bit.ly/gxyRNASEX RNA-Seq Example]
+
: An introduction to NGS processing (specifically RNA-Seq) with [[Galaxy]].
+
; [http://www.openhelix.com/cgi/tutorialInfo.cgi?id=82 OpenHelix Galaxy User Tutorial]
+
: A Flash based tutorial on using Galaxy.  Provided by [http://www.openhelix.com OpenHelix].  Tutorial includes slides, handouts and exercises.  Requires subscription.
+
 
|getting started preamble=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.
 
|getting started preamble=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.
  
Full documentation on all aspects of getting, installing, and using Galaxy is available from the [http://wiki.g2.bx.psu.edu/ Galaxy Wiki].
+
Full documentation on all aspects of getting, installing, and using Galaxy is available from the [https://galaxyproject.org/ Galaxy Community Hub].
|req=
+
|doc=*[https://galaxyproject.org/learn User documentation]
|install=
+
*[https://docs.galaxyproject.org/  Source code documentation]
|config=
+
*[https://galaxyproject.org/search/ Search the whole universe of Galaxy docs]
|doc=
+
|survey link=Galaxy
*[http://wiki.galaxyproject.org/ General Galaxy info]
+
|contact email=[mailto:clements@galaxyproject.org Dave Clements] or [mailto:outreach@galaxyproject.org Galaxy Outreach]
*[http://wiki.galaxyproject.org/Learn User documentation]
+
*[http://galaxy-dist.readthedocs.org/  Source code documentation]
+
*[http://galaxyproject.org/search/ Search the whole universe of Galaxy docs]
+
|dev ppl=The [http://wiki.galaxyproject.org/GalaxyTeam Galaxy Development Team] are listed on the Galaxy wiki; in addition to the core developers, there are also extensive contributions from the Galaxy user community.
+
 
|dev status=
 
|dev status=
|dl tracking=
 
|logo info=
 
|see also=
 
|extra=
 
 
}}
 
}}
 +
<!-- extra links:
 +
<div class="compBoxHdr">Resources</div>
 +
*[https://galaxyproject.org Home Page]
 +
*[https://galaxyproject.org/use Galaxy Platforms Directory]
 +
*[https://galaxyproject.org/ Galaxy Community Hub]
 +
*[http://getgalaxy.org Get your own Galaxy]
 +
*[http://galaxyproject.org/search Search]
 +
<hr />
 +
{{GalaxyEventsBoxItem}}
 +
-->
 +
 +
 +
 +
 +
  
 
{{SemanticLink
 
{{SemanticLink
|linkurl=http://getgalaxy.org
+
|linkurl=http://getgalaxy.org/
 
|linktype=download
 
|linktype=download
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
|linkurl=https://bitbucket.org/galaxy/
+
|linkurl=https://github.com/galaxyproject/galaxy/
 
|linktype=source code
 
|linktype=source code
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
|linkurl=http://galaxy-dist.readthedocs.org/
+
|linkurl=https://docs.galaxyproject.org
 +
|linktitle=Galaxy source code documentation
 
|linktype=documentation
 
|linktype=documentation
|linktitle=Galaxy source code documentation
 
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
|linkurl=http://galaxyproject.org/
+
|linkurl=https://galaxyproject.org/
 
|linktype=website
 
|linktype=website
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
|linkurl=http://wiki.galaxyproject.org/
+
|linkurl=https://galaxyproject.org/
 
|linktype=documentation
 
|linktype=documentation
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=https://twitter.com/galaxyproject
 
|linkurl=https://twitter.com/galaxyproject
 
|linktype=social media
 
|linktype=social media
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
|linkurl=http://www.citeulike.org/group/16008/  
+
|linkurl=https://www.zotero.org/groups/1732893/galaxy
 +
|linktitle=Galaxy publication library
 
|linktype=other
 
|linktype=other
|linktitle=Galaxy bibliography on Cite-U-Like
 
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
|linkurl=http://www.mendeley.com/groups/1710745/
+
|linkurl=https://galaxyproject.org/use/
|linktype=other
+
|linktitle=Galaxy bibliography on Mendeley
+
}}
+
 
+
{{SemanticLink
+
|linkurl=https://trello.com/board/galaxy-development-inbox/50686d0302dfa79d13d90c45
+
|linktype=other
+
|linktitle=Galaxy Trello board
+
}}
+
 
+
{{SemanticLink
+
|linkurl=http://usegalaxy.org/
+
 
|linktype=public server
 
|linktype=public server
|linkdesc=A fully-fledged, fully-supported instance
+
|linkdesc=Fully supported, publicly accessible platforms for using Galaxy
 
}}
 
}}
 
{{SemanticLink
 
|linkurl=https://test.g2.bx.psu.edu/
 
|linkdesc=Test instance
 
|linktype=demo server
 
}}
 
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://wiki.galaxyproject.org/PublicGalaxyServers
 
|linkurl=http://wiki.galaxyproject.org/PublicGalaxyServers
 +
|linktitle=ully supported, publicly accessible platforms for using Galaxy
 
|linktype=wild URL
 
|linktype=wild URL
|linktitle=List of public Galaxy servers
 
 
}}
 
}}
 
+
{{SemanticLink
 
+
|linkurl=https://galaxyproject.github.io
 
+
|linktitle=List of Galaxy Produced Software
<!-- extra links:
+
|linktype=documentation
<div class="compBoxHdr">Resources</div>
+
}}
*[http://galaxyproject.org Home Page]
+
*[http://usegalaxy.org Public Server]
+
*[http://wiki.galaxyproject.org/ Galaxy Wiki]
+
*[http://getgalaxy.org Download / Cloud]
+
*[[Galaxy Tutorial]]
+
*[http://galaxyproject.org/search Search]
+
*[http://wiki.galaxyproject.org/Community/GalaxyAdmins/SurveyResults 2012 Survey]
+
<hr />
+
{{GalaxyEventsBoxItem}}
+
-->
+
  
 
[[Category:Analysis]]
 
[[Category:Analysis]]
[[Category:Comparative Genomics]]
 
[[Category:GMOD Components]]
 
 
[[Category:Annotation]]
 
[[Category:Annotation]]
 +
[[Category:Comparative_Genomics]]
 +
[[Category:GMOD_Components]]
 
[[Category:Galaxy]]
 
[[Category:Galaxy]]

Latest revision as of 19:43, 13 December 2018

Galaxy logo
Status
  • Mature release
  • Development: active
  • Support: active
Licence
{{{PAGENAME}}} is open source

Academic Free License 3.0

Resources


About Galaxy

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 and is available on a wide variety of platforms and publicly accessible websites. Galaxy servers make 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.


link=https://galaxyproject.org/events/gcc2019/ 2019 Galaxy Community Conference

2019 Galaxy Community Conference

The 2019 Galaxy Community Conference (GCC2019) will be held 1-6 July, in Freiburg Germany. Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it.  The 2019 conference includes training that offers in-depth topic coverage across several concurrent sessions, and a CollaborationFest.


Visit the Galaxy website.

Screenshots

Galaxy 'Upload file' tool
Galaxy 'Table Browser' tool
Editing the attributes of a data set in Galaxy

Downloads

Using Galaxy

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.

Full documentation on all aspects of getting, installing, and using Galaxy is available from the Galaxy Community Hub.


Documentation

Publications, Tutorials, and Presentations

Publications on or mentioning Galaxy

See Citing Galaxy for a core list of 25+ papers on Galaxy, and the Galaxy publication library for a fuller list of papers mentioning or using Galaxy.

Tutorials

A wealth of community created and maintained training materials are available:


Contacts and Mailing Lists

Mailing List Link Description Archive(s)
Galaxy
(Search everything)
galaxy-announce Announcements of interest to the Galaxy community. Low volume and moderated. Nabble, Mailman
Galaxy Help General questions and discussion about using Galaxy. Also used for announcements relevant to the Galaxy user community. This is not a mailing list, but an online forum, based on the popular Discourse platform. High volume.
galaxy-dev Discussion and questions regarding local installations and development of Galaxy. Medium volume. Nabble, Mailman

Galaxy in the wild

Public installations of Galaxy:



More on Galaxy

See Category:Galaxy


Facts about "Galaxy"RDF feed
Available on platformweb +
Has URLhttp://getgalaxy.org/ +, https://github.com/galaxyproject/galaxy/ +, https://docs.galaxyproject.org +, https://galaxyproject.org/ +, https://twitter.com/galaxyproject +, https://www.zotero.org/groups/1732893/galaxy +, https://galaxyproject.org/use/ +, http://wiki.galaxyproject.org/PublicGalaxyServers + and https://galaxyproject.github.io +
Has descriptionGalaxy is an 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 and is available on a wide variety of platforms and publicly accessible websites. Galaxy servers make 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.


link=https://galaxyproject.org/events/gcc2019/ 2019 Galaxy Community Conference

2019 Galaxy Community Conference[edit]

The 2019 Galaxy Community Conference (GCC2019) will be held 1-6 July, in Freiburg Germany. Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it.  The 2019 conference includes training that offers in-depth topic coverage across several concurrent sessions, and a CollaborationFest.
current sessions, and a CollaborationFest. + and Fully supported, publicly accessible platforms for using Galaxy +
Has development statusactive +
Has input formatRoadmaps +, Sequences +, ab1 +, affybatch +, afg +, axt +, bam +, bcf +, bed +, bedgraph +, bigbed +, bigwig +, bowtie_base_index +, bowtie_color_index +, chrint +, cisml +, csfasta +, csv +, eland +, elandmulti +, encodepeak +, eset +, fasta +, fastq +, fastqcssanger +, fastqillumina +, fastqsanger +, fastqsolexa +, fli +, fped +, fphe +, fqtoc +, gatk_dbsnp +, gatk_interval +, gatk_recal +, gatk_report +, gatk_tranche +, gd_indivs +, gd_ped +, gd_sap +, gd_snp +, GFF +, GFF3 +, gtf +, interval +, lav +, ldindep +, len +, linecount +, lped +, maf +, malist +, memexml +, nex +, nhx +, pbed +, phyloxml +, picard_interval_list +, pileup +, pphe +, qual454 +, qualillumina +, qualsolexa +, qualsolid +, sam +, scf +, sff +, snpmatrix +, snptest +, tabular +, taxonomy +, twobit +, txt +, vcf +, velvet +, wig + and xml +
Has licenceAcademic Free License 3.0 +
Has logoGalaxyLogoBigger.png +
Has output formatzillions! +
Has software maturity statusmature +
Has support statusactive +
Has titleGalaxy source code documentation +, Galaxy publication library +, ully supported, publicly accessible platforms for using Galaxy + and List of Galaxy Produced Software +
Has topicGalaxy +
Is open sourceYes +
Link typedownload +, source code +, documentation +, website +, social media +, other +, public server + and wild URL +
Release date2005 +
Tool functionality or classificationGenome Visualization and Editing +, Workflow Management +, Tool Integration + and Analysis +
Written in languagePython + and XML +
Has subobjectThis property is a special property in this wiki.Galaxy#http://getgalaxy.org/ +, Galaxy#https://github.com/galaxyproject/galaxy/ +, Galaxy#https://docs.galaxyproject.org +, Galaxy#https://galaxyproject.org/ +, Galaxy#https://twitter.com/galaxyproject +, Galaxy#https://www.zotero.org/groups/1732893/galaxy +, Galaxy#https://galaxyproject.org/use/ +, Galaxy#http://wiki.galaxyproject.org/PublicGalaxyServers + and Galaxy#https://galaxyproject.github.io +