Difference between revisions of "Galaxy"

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{{ImageCenter|GalaxyLogoBigger.png|Galaxy||http://getgalaxy.org/}}
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{{Tool data
__NOTITLE__
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|name=Galaxy
 
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|status=mature
{{ComponentBox|{{GalaxyResourcesBoxItem}}|{{ComponentBoxEventsHeader}}|{{#icon: GCC2012Logo.png|2012 Galaxy Community Conference|170|http://galaxyproject.org/wiki/Events/GCC2012}}<hr />|{{GalaxyEventsBoxItem}}||}}
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|dev=active
 
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|support=active
[http://usegalaxy.org Galaxy] is an open, web-based platform for ''accessible, reproducible, and transparent'' computational biomedical research.
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|type=Genome Visualization and Editing, Workflow Management, Tool Integration, Analysis
 +
|platform=web
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|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 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.
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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.
 
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__TOC__
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== 2012 Galaxy Community Conference ==
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[[File:GCC2019Logo.png|left|250px|link=https://galaxyproject.org/events/gcc2019/ 2019 Galaxy Community Conference]]
  
{{ImageLeft|GCC2012Logo.png|2012 Galaxy Community Conference|200|http://galaxyproject.org/wiki/Events/GCC2012}}
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=== 2019 Galaxy Community Conference ===
The [http://galaxyproject.org/wiki/Events/GCC2012 2012 Galaxy Community Conference (GCC2012)] will be July 25-27 at the [http://uic.edu University of Illinois at Chicago (UIC)].  The event is being hosted by UIC, the [http://illinois.edu/ University of Illinois at Urbana-Champaign (UIUC)] and [http://anl.gov/|Argonne National Laboratory].
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[http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts Abstract submission] and [http://wiki.g2.bx.psu.edu/Events/GCC2012/Register registration] will open in 2012.
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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.
  
[http://galaxy.psu.edu/gcc2011/ GCC2011] had almost 150 registrations and the conference featured [http://galaxy.psu.edu/gcc2011/Programme.html two full days] of presentations (now available on video) 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.  For 2012 we are adding a training day at the start, and we expect even more participants.  We are also encouraging [http://wiki.g2.bx.psu.edu/Events/GCC2012/Sponsorships sponsorships] this year.
 
  
==Demo & Screencasts ==
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|open source=Yes
 +
|licence=[http://opensource.org/licenses/AFL-3.0 Academic Free License 3.0]
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|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
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|output=zillions!
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|language=Python, XML
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|audience=public,private
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|release date=2005
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|use template=Yes
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|logo=GalaxyLogoBigger.png
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|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]]
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|mail={{MailingListsFor|Galaxy}}
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|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.
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|tutorials=;
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:A wealth of community created and maintained training materials are available:
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:*[https://training.galaxyproject.org Galaxy Training website]
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|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.
  
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.
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Full documentation on all aspects of getting, installing, and using Galaxy is available from the [https://galaxyproject.org/ Galaxy Community Hub].
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|doc=*[https://galaxyproject.org/learn User documentation]
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*[https://docs.galaxyproject.org/  Source code documentation]
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*[https://galaxyproject.org/search/ Search the whole universe of Galaxy docs]
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|survey link=Galaxy
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|contact email=[mailto:clements@galaxyproject.org Dave Clements] or [mailto:outreach@galaxyproject.org Galaxy Outreach]
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|dev status=
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}}
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<!-- extra links:
 +
<div class="compBoxHdr">Resources</div>
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*[https://galaxyproject.org Home Page]
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*[https://galaxyproject.org/use Galaxy Platforms Directory]
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*[https://galaxyproject.org/ Galaxy Community Hub]
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*[http://getgalaxy.org Get your own Galaxy]
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*[http://galaxyproject.org/search Search]
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<hr />
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{{GalaxyEventsBoxItem}}
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-->
  
==Documentation==
 
  
* Most Galaxy documentation is in the [http://wiki.g2.bx.psu.edu/ 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
 
  
== Mailing Lists ==
 
  
{{MailingListsFor|Galaxy}}
 
  
==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 at [http://getgalaxy.org/ GetGalaxy.org].
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{{SemanticLink
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|linkurl=http://getgalaxy.org/
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|linktype=download
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}}
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{{SemanticLink
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|linkurl=https://github.com/galaxyproject/galaxy/
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|linktype=source code
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}}
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{{SemanticLink
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|linkurl=https://docs.galaxyproject.org
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|linktitle=Galaxy source code documentation
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|linktype=documentation
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}}
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{{SemanticLink
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|linkurl=https://galaxyproject.org/
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|linktype=website
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}}
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{{SemanticLink
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|linkurl=https://galaxyproject.org/
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|linktype=documentation
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}}
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{{SemanticLink
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|linkurl=https://twitter.com/galaxyproject
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|linktype=social media
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}}
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{{SemanticLink
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|linkurl=https://www.zotero.org/groups/1732893/galaxy
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|linktitle=Galaxy publication library
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|linktype=other
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}}
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{{SemanticLink
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|linkurl=https://galaxyproject.org/use/
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|linktype=public server
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|linkdesc=Fully supported, publicly accessible platforms for using Galaxy
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}}
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{{SemanticLink
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|linkurl=http://wiki.galaxyproject.org/PublicGalaxyServers
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|linktitle=ully supported, publicly accessible platforms for using Galaxy
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|linktype=wild URL
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}}
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{{SemanticLink
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|linkurl=https://galaxyproject.github.io
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|linktitle=List of Galaxy Produced Software
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|linktype=documentation
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}}
  
 
[[Category:Analysis]]
 
[[Category:Analysis]]
[[Category:Comparative Genomics]]
 
[[Category:GMOD Components]]
 
 
[[Category:Annotation]]
 
[[Category:Annotation]]
 +
[[Category:Comparative_Genomics]]
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[[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 +