Galaxy/tool data

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{{ {{{template}}} | name = Galaxy | full_name = | status = mature | dev = active | support = active | type = Genome Visualization and Editing, Workflow Management, Tool Integration, Analysis | platform = web | logo = GalaxyLogoBigger.png | home = http://galaxyproject.org | about = 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.

| screenshot =

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

| public_server = http://usegalaxy.org | dl = | dl_url = http://getgalaxy.org | dl_src = | dl_src_url = https://bitbucket.org/galaxy/ | dl_dev = | dl_dev_url = | 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 Galaxy Wiki. | req = | install = | config = | doc =

| papers = 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. | presentations = | 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.

| wild_urls = Galaxy maintains a list of public Galaxy servers | mail =

Mailing List Link Description Archive(s)
Galaxy
(Search Announce, Dev, Galaxy Biostar, Proteomics & France)
galaxy-announce Announcements of interest to the Galaxy community. Low volume and moderated. Nabble, Mailman
galaxy-dev Discussion and questions regarding local installations and development of Galaxy. High volume. Nabble, GMane, Mail-Archive.com, OSDir, Mailman
Galaxy Biostar 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 Biostar platform. High volume. Galaxy Biostar has an archive of all postings, and also any threads that were posted to the galaxy-user mailing list that it replaced. Galaxy-user only archives are available at Nabble, GMane (2011-14), Mail-Archive.com (2012-14), OSDir (2006-14), Mailman (2006-14)
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

| logo_info = | dev_ppl = The 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 = | contact_email = Dave Clements or Galaxy Outreach | 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! | see_also = | demo_server = http://usegalaxy.org/ | survey_link = Galaxy | extras = |release date=2005 }}