Difference between revisions of "Galaxy"
m |
m |
||
(35 intermediate revisions by 3 users not shown) | |||
Line 1: | Line 1: | ||
− | {{ | + | {{Tool data |
− | + | |name=Galaxy | |
− | + | |status=mature | |
− | + | |dev=active | |
− | + | |support=active | |
− | [http://usegalaxy.org Galaxy] is an open, web-based platform for ''accessible, reproducible, and transparent'' computational biomedical research. | + | |type=Genome Visualization and Editing, Workflow Management, Tool Integration, Analysis |
+ | |platform=web | ||
+ | |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. | ||
* ''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 | + | 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. |
− | + | [[File:GCC2016Logo.png|left|250px|link=https://gcc2016.iu.edu/|2016 Galaxy Community Conference]] | |
+ | === 2016 Galaxy Community Conference === | ||
− | + | The [https://gcc2016.iu.edu/ 2016 Galaxy Community Conference (GCC2016)] will be held June 25-29, at [https://gcc2016.iu.edu/location/ Indiana University] in Bloomington, Indiana, United states, immediately before the [[Jun 2016 GMOD Meeting|June 2016 GMOD Meeting]], also in Bloomington. | |
− | + | 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 also includes [https://gcc2016.iu.edu/training two days of training] offering in-depth topic coverage across several concurrent sessions, and [https://gcc2016.iu.edu/hacks/ two days of hackathons]. | |
− | + | ||
− | |||
− | |||
− | == | + | |open source=Yes |
+ | |licence=[http://opensource.org/licenses/AFL-3.0 Academic Free License 3.0] | ||
+ | |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! | ||
+ | |language=Python, XML | ||
+ | |audience=public,private | ||
+ | |release date=2005 | ||
+ | |use template=Yes | ||
+ | |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]] | ||
+ | |mail={{MailingListsFor|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=;[[Galaxy Tutorial]] | ||
+ | :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. | ||
− | + | Full documentation on all aspects of getting, installing, and using Galaxy is available from the [https://wiki.galaxyproject.org/ Galaxy Wiki]. | |
+ | |doc=*[http://wiki.galaxyproject.org/ General Galaxy info] | ||
+ | *[http://wiki.galaxyproject.org/Learn User documentation] | ||
+ | *[http://docs.galaxyproject.org/ Source code documentation] | ||
+ | *[http://galaxyproject.org/search/ Search the whole universe of Galaxy docs] | ||
+ | |survey link=Galaxy | ||
+ | |contact email=[mailto:clements@galaxyproject.org Dave Clements] or [mailto:outreach@galaxyproject.org Galaxy Outreach] | ||
+ | |dev status= | ||
+ | }} | ||
+ | <!-- 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}} | ||
+ | --> | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | Galaxy | + | {{SemanticLink |
+ | |linkurl=http://getgalaxy.org | ||
+ | |linktype=download | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=https://github.com/galaxyproject/galaxy/ | ||
+ | |linktype=source code | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=https://docs.galaxyproject.org | ||
+ | |linktitle=Galaxy source code documentation | ||
+ | |linktype=documentation | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://galaxyproject.org/ | ||
+ | |linktype=website | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://wiki.galaxyproject.org/ | ||
+ | |linktype=documentation | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=https://twitter.com/galaxyproject | ||
+ | |linktype=social media | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://www.citeulike.org/group/16008/ | ||
+ | |linktitle=Galaxy bibliography on Cite-U-Like | ||
+ | |linktype=other | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://www.mendeley.com/groups/1710745/ | ||
+ | |linktitle=Galaxy bibliography on Mendeley | ||
+ | |linktype=other | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=https://trello.com/board/galaxy-development-inbox/50686d0302dfa79d13d90c45 | ||
+ | |linktitle=Galaxy Trello board | ||
+ | |linktype=other | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://usegalaxy.org/ | ||
+ | |linktype=public server | ||
+ | |linkdesc=A fully-fledged, fully-supported instance | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=https://test.g2.bx.psu.edu/ | ||
+ | |linktype=demo server | ||
+ | |linkdesc=Test instance | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://wiki.galaxyproject.org/PublicGalaxyServers | ||
+ | |linktitle=List of public Galaxy servers | ||
+ | |linktype=wild URL | ||
+ | }} | ||
+ | {{SemanticLink | ||
+ | |linkurl=https://galaxyproject.github.io | ||
+ | |linktitle=List of Galaxy Produced Softawre | ||
+ | |linktype=documentation | ||
+ | }} | ||
[[Category:Analysis]] | [[Category:Analysis]] |
Revision as of 18:55, 26 February 2016
- Mature release
- Development: active
- Support: active
Contents
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.
2016 Galaxy Community Conference
The 2016 Galaxy Community Conference (GCC2016) will be held June 25-29, at Indiana University in Bloomington, Indiana, United states, immediately before the June 2016 GMOD Meeting, also in Bloomington.
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 also includes two days of training offering in-depth topic coverage across several concurrent sessions, and two days of hackathons.
Visit the Galaxy website.
Screenshots
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
- General Galaxy info
- User documentation
- Source code documentation
- Search the whole universe of Galaxy docs
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. Medium volume. | Nabble, Mailman |
Galaxy in the wild
Public installations of Galaxy:
More on Galaxy
See Category:Galaxy
Available on platform | web + |
Has URL | http://getgalaxy.org +, https://github.com/galaxyproject/galaxy/ +, https://docs.galaxyproject.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/ +, http://wiki.galaxyproject.org/PublicGalaxyServers + and https://galaxyproject.github.io + |
Has description | Galaxy is an open, … Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.
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.
2016 Galaxy Community Conference[edit]The 2016 Galaxy Community Conference (GCC2016) will be held June 25-29, at Indiana University in Bloomington, Indiana, United states, immediately before the June 2016 GMOD Meeting, also in Bloomington. 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 also includes two days of training offering in-depth topic coverage across several concurrent sessions, and two days of hackathons.016.iu.edu/hacks/ two days of hackathons]. +, A fully-fledged, fully-supported instance + and Test instance + |
Has development status | active + |
Has input format | 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 + and xml + |
Has licence | Academic Free License 3.0 + |
Has logo | GalaxyLogoBigger.png + |
Has output format | zillions! + |
Has software maturity status | mature + |
Has support status | active + |
Has title | Galaxy source code documentation +, Galaxy bibliography on Cite-U-Like +, Galaxy bibliography on Mendeley +, Galaxy Trello board +, List of public Galaxy servers + and List of Galaxy Produced Softawre + |
Has topic | Galaxy + |
Is open source | Yes + |
Link type | download +, source code +, documentation +, website +, social media +, other +, public server +, demo server + and wild URL + |
Release date | 2005 + |
Tool functionality or classification | Genome Visualization and Editing +, Workflow Management +, Tool Integration + and Analysis + |
Written in language | Python + 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#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/ +, Galaxy#http://wiki.galaxyproject.org/PublicGalaxyServers + and Galaxy#https://galaxyproject.github.io + |