Difference between revisions of "Galaxy"

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m (Adding GAW and GCC)
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{{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=[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.
 
* ''Accessibility:'' Galaxy enables users without programming experience to easily specify parameters and run tools and workflows.
Line 36: Line 35:
 
[http://australianbioinformatics.net/gaw-2014 Registration is open].  Registration is also ''free, but space is limited.''
 
[http://australianbioinformatics.net/gaw-2014 Registration is open].  Registration is also ''free, but space is limited.''
 
   
 
   
Participants who wish to give presentations or present posters (potentially with technical demonstrations) that showcase use of Galaxy should [http://australianbioinformatics.net/gaw-2014 submit an abstract and brief one-paragraph bio] '''by February 15th, 2014'''. Submitters will be notified by February 28th. Speakers, panelists, and poster presenters will be selected by the program committee based on relevance to symposium objectives and workshop balance.  
+
Participants who wish to give presentations or present posters (potentially with technical demonstrations) that showcase use of Galaxy should [http://australianbioinformatics.net/gaw-2014 submit an abstract and brief one-paragraph bio] '''by February 15th, 2014'''. Submitters will be notified by February 28th. Speakers, panelists, and poster presenters will be selected by the program committee based on relevance to symposium objectives and workshop balance.
|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 [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.
 
|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.
|presentations=
 
 
|tutorials=;[[Galaxy Tutorial]]
 
|tutorials=;[[Galaxy Tutorial]]
 
:As taught at the [[2013 GMOD Summer School]]
 
:As taught at the [[2013 GMOD Summer School]]
Line 67: Line 64:
 
|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://wiki.galaxyproject.org/ Galaxy Wiki].
|req=
+
|doc=*[http://wiki.galaxyproject.org/ General Galaxy info]
|install=
+
|config=
+
|doc=
+
*[http://wiki.galaxyproject.org/ General Galaxy info]
+
 
*[http://wiki.galaxyproject.org/Learn User documentation]
 
*[http://wiki.galaxyproject.org/Learn User documentation]
 
*[http://galaxy-dist.readthedocs.org/  Source code documentation]
 
*[http://galaxy-dist.readthedocs.org/  Source code documentation]
 
*[http://galaxyproject.org/search/ Search the whole universe of Galaxy docs]
 
*[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.
+
|survey link=Galaxy
 +
|contact email=[mailto:clements@galaxyproject.org Dave Clements] or [mailto:outreach@galaxyproject.org Galaxy Outreach]
 
|dev status=
 
|dev status=
|dl tracking=
 
|logo info=
 
|see also=
 
|extra=
 
|use template=yes
 
 
}}
 
}}
 +
<!-- extra links:
 +
<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:Comparative Genomics]]
 +
[[Category:GMOD Components]]
 +
[[Category:Annotation]]
 +
[[Category:Galaxy]]
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://getgalaxy.org
 
|linkurl=http://getgalaxy.org
 
|linktype=download
 
|linktype=download
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=https://bitbucket.org/galaxy/
 
|linkurl=https://bitbucket.org/galaxy/
 
|linktype=source code
 
|linktype=source code
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://galaxy-dist.readthedocs.org/
 
|linkurl=http://galaxy-dist.readthedocs.org/
 +
|linktitle=Galaxy source code documentation
 
|linktype=documentation
 
|linktype=documentation
|linktitle=Galaxy source code documentation
 
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://galaxyproject.org/
 
|linkurl=http://galaxyproject.org/
 
|linktype=website
 
|linktype=website
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://wiki.galaxyproject.org/
 
|linkurl=http://wiki.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=http://www.citeulike.org/group/16008/
 +
|linktitle=Galaxy bibliography on Cite-U-Like
 
|linktype=other
 
|linktype=other
|linktitle=Galaxy bibliography on Cite-U-Like
 
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://www.mendeley.com/groups/1710745/
 
|linkurl=http://www.mendeley.com/groups/1710745/
 +
|linktitle=Galaxy bibliography on Mendeley
 
|linktype=other
 
|linktype=other
|linktitle=Galaxy bibliography on Mendeley
 
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=https://trello.com/board/galaxy-development-inbox/50686d0302dfa79d13d90c45
 
|linkurl=https://trello.com/board/galaxy-development-inbox/50686d0302dfa79d13d90c45
 +
|linktitle=Galaxy Trello board
 
|linktype=other
 
|linktype=other
|linktitle=Galaxy Trello board
 
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://usegalaxy.org/
 
|linkurl=http://usegalaxy.org/
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|linkdesc=A fully-fledged, fully-supported instance
 
|linkdesc=A fully-fledged, fully-supported instance
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=https://test.g2.bx.psu.edu/
 
|linkurl=https://test.g2.bx.psu.edu/
 +
|linktype=demo server
 
|linkdesc=Test instance
 
|linkdesc=Test instance
|linktype=demo server
 
 
}}
 
}}
 
 
{{SemanticLink
 
{{SemanticLink
 
|linkurl=http://wiki.galaxyproject.org/PublicGalaxyServers
 
|linkurl=http://wiki.galaxyproject.org/PublicGalaxyServers
 +
|linktitle=List of public Galaxy servers
 
|linktype=wild URL
 
|linktype=wild URL
|linktitle=List of public Galaxy servers
 
 
}}
 
}}
 
 
 
<!-- extra links:
 
<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:Comparative Genomics]]
 
[[Category:GMOD Components]]
 
[[Category:Annotation]]
 
[[Category:Galaxy]]
 

Revision as of 00:27, 22 November 2014

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. The 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 downloading the Galaxy application and customizing it to meet particular needs.


2014 Galaxy Community Conference

2014 Galaxy Community Conference

The 2014 Galaxy Community Conference (GCC2013) will be held June 30 through July 2, at the Homewood Campus of Johns Hopkins University], in 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 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.


Galaxy Australasia Workshop 2014 (GAW 2014)

1st Galaxy Australasia Workshop 2014 (GAW 2014)

The 1st Galaxy Australasia Workshop 2014 (GAW 2014) will be held in Melbourne, Australia on 24 and 25th March 2014.

The Galaxy Australasia Workshop is a great opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes and lightning talks, all about ways of using Galaxy for high-throughput biology, imaging and other scientific applications. The workshop will also include Training Sessions taught by Galaxy developers and master users. GAW 2014 will run 24 and 25th March, immediately preceding Computational and Simulation Sciences and eResearch in Melbourne.

GAW 2014 will also include poster session, keynote speakers.

Registration is open. Registration is also free, but space is limited.

Participants who wish to give presentations or present posters (potentially with technical demonstrations) that showcase use of Galaxy should submit an abstract and brief one-paragraph bio by February 15th, 2014. Submitters will be notified by February 28th. Speakers, panelists, and poster presenters will be selected by the program committee based on relevance to symposium objectives and workshop balance.


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 Wiki.


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 CiteULike group for a fuller list of papers mentioning or using Galaxy.

Tutorials

Galaxy Tutorial
As taught at the 2013 GMOD Summer School
Galaxy Learning Hub
A wealth of training materials, including:
RNA-Seq Example
An introduction to NGS processing (specifically RNA-Seq) with Galaxy.
OpenHelix Galaxy User Tutorial
A Flash based tutorial on using Galaxy. Provided by OpenHelix. Tutorial includes slides, handouts and exercises. Requires subscription.


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. High volume. Nabble, Mailman
galaxy-proteomics General questions and discussion regarding proteomics in Galaxy. Low volume. Nabble, Mailman
galaxy-france Cette liste est destinée à l'information (et aux discussions) de la Communauté francaise Galaxy. (This list is for announcements to (and discussion within) the French Galaxy Community. Most list content is in French.) Faible volume / Low volume. Nabble
galaxy-commits Galaxy source control commit messages. 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://bitbucket.org/galaxy/ +, http://galaxy-dist.readthedocs.org/ +, http://galaxyproject.org/ +, http://wiki.galaxyproject.org/ +, https://twitter.com/galaxyproject +, http://www.citeulike.org/group/16008/ +, http://www.mendeley.com/groups/1710745/ +, https://trello.com/board/galaxy-development-inbox/50686d0302dfa79d13d90c45 +, http://usegalaxy.org/ +, https://test.g2.bx.psu.edu/ + and http://wiki.galaxyproject.org/PublicGalaxyServers +
Has descriptionGalaxy is an open, 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 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 downloading the Galaxy application and customizing it to meet particular needs.


2014 Galaxy Community Conference[edit]

2014 Galaxy Community Conference

The 2014 Galaxy Community Conference (GCC2013) will be held June 30 through July 2, at the Homewood Campus of Johns Hopkins University], in 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 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.


Galaxy Australasia Workshop 2014 (GAW 2014)[edit]

1st Galaxy Australasia Workshop 2014 (GAW 2014)

The 1st Galaxy Australasia Workshop 2014 (GAW 2014) will be held in Melbourne, Australia on 24 and 25th March 2014.

The Galaxy Australasia Workshop is a great opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes and lightning talks, all about ways of using Galaxy for high-throughput biology, imaging and other scientific applications. The workshop will also include Training Sessions taught by Galaxy developers and master users. GAW 2014 will run 24 and 25th March, immediately preceding Computational and Simulation Sciences and eResearch in Melbourne.

GAW 2014 will also include poster session, keynote speakers.

Registration is open. Registration is also free, but space is limited.

Participants who wish to give presentations or present posters (potentially with technical demonstrations) that showcase use of Galaxy should submit an abstract and brief one-paragraph bio by February 15th, 2014. Submitters will be notified by February 28th. Speakers, panelists, and poster presenters will be selected by the program committee based on relevance to symposium objectives and workshop balance.
symposium objectives and workshop balance. +, A fully-fledged, fully-supported instance + and Test instance +
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 bibliography on Cite-U-Like +, Galaxy bibliography on Mendeley +, Galaxy Trello board + and List of public Galaxy servers +
Has topicGalaxy +
Is open sourceYes +
Link typedownload +, source code +, documentation +, website +, social media +, other +, public server +, demo 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://bitbucket.org/galaxy/ +, Galaxy#http://galaxy-dist.readthedocs.org/ +, Galaxy#http://galaxyproject.org/ +, Galaxy#http://wiki.galaxyproject.org/ +, Galaxy#https://twitter.com/galaxyproject +, Galaxy#http://www.citeulike.org/group/16008/ +, Galaxy#http://www.mendeley.com/groups/1710745/ +, Galaxy#https://trello.com/board/galaxy-development-inbox/50686d0302dfa79d13d90c45 +, Galaxy#http://usegalaxy.org/ +, Galaxy#https://test.g2.bx.psu.edu/ + and Galaxy#http://wiki.galaxyproject.org/PublicGalaxyServers +