Difference between revisions of "Galaxy/tool data"

From GMOD
Jump to: navigation, search
m (Text replace - "{{GMODSchool}} " to "")
m
Line 2: Line 2:
 
| name = Galaxy
 
| name = Galaxy
 
| full_name =  
 
| full_name =  
| status = release
+
| status = mature
 
| dev = active
 
| dev = active
 
| support = active
 
| support = active

Revision as of 22:11, 20 August 2013

{{ {{{template}}} | name = Galaxy | full_name = | status = mature | dev = active | support = active | type = Genome Visualization and Editing, Workflow Management, Tool Integration, Analysis | os_web = y | 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.

2013 Galaxy Community Conference

2013 Galaxy Community Conference

The 2013 Galaxy Community Conference (GCC2013) was held June 30 through July 2 at the University of Oslo in Oslo, Norway. GCC2013 featured a Tutorial Day followed by two days of presentations, discussions, lightning talks, breakouts, and keynotes 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.

Slides, videos, posters, and Training Day material are now linked to from the conference web site.

GCC2014 will be held in Baltimore, Maryland, United States in the sumer of 2014.

| 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 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

| 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 = }}