Difference between revisions of "Galaxy/tool data"
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| name = Galaxy | | name = Galaxy | ||
| full_name = | | full_name = | ||
| − | | status = | + | | status = release |
| − | | dev = active | + | | dev = active |
| − | | | + | | support = active |
| + | | type = Genome Visualization and Editing, Workflow Management, Tool Integration, Analysis | ||
| + | | os_web = y | ||
| logo = GalaxyLogoBigger.png | | logo = GalaxyLogoBigger.png | ||
| − | | home = http:// | + | | home = http://galaxyproject.org |
| 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 13: | Line 15: | ||
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. | 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. | ||
| + | |||
| + | === 2013 Galaxy Community Conference === | ||
| + | |||
| + | [[File:GCC2013Logo.png|left|200px|link=http://wiki.galaxyproject.org/Events/GCC2013|2013 Galaxy Community Conference]] | ||
| + | |||
| + | The [http://wiki.galaxyproject.org/Events/GCC2013 2013 Galaxy Community Conference (GCC2013)] will be held June 30 through July 2 at the University of Oslo in Oslo, Norway. GCC2013 will feature 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. | ||
| + | |||
| + | [http://wiki.galaxyproject.org/Events/GCC2012 GCC2012] was held in Chicago had over 200 attendees. Slides and videos of all talks at [http://wiki.galaxyproject.org/Events/GCC2012 GCC2012] and [http://wiki.galaxyproject.org/Events/GCC2011 GCC2011] are available on the Galaxy wiki. | ||
| screenshot = | | 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]] | ||
| public_server = http://usegalaxy.org | | public_server = http://usegalaxy.org | ||
| − | | dl = | + | | dl = |
| − | + | | dl_url = http://getgalaxy.org | |
| dl_src = | | dl_src = | ||
| + | | dl_src_url = https://bitbucket.org/galaxy/ | ||
| dl_dev = | | dl_dev = | ||
| − | | getting_started_preamble = | + | | 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 [http://wiki.g2.bx.psu.edu/ Galaxy Wiki]. | ||
| req = | | req = | ||
| install = | | install = | ||
| config = | | config = | ||
| − | | doc = | + | | doc = |
| − | + | *[http://wiki.galaxyproject.org/ General Galaxy info] | |
| − | * [ | + | *[http://wiki.galaxyproject.org/Learn User documentation] |
| − | + | *[http://galaxy-dist.readthedocs.org/ Source code documentation] | |
| + | *[http://galaxyproject.org/search/ Search the whole universe of Galaxy docs] | ||
| + | | 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 = | | presentations = | ||
| − | | tutorials = | + | | tutorials = |
| − | | wild_urls = | + | ;[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!] | ||
| + | ;[[Galaxy Tutorial]] | ||
| + | :As taught at the [[2012 GMOD Summer School]] | ||
| + | | wild_urls = Galaxy maintains a list of [http://wiki.galaxyproject.org/PublicGalaxyServers public Galaxy servers] | ||
| mail = {{MailingListsFor|Galaxy}} | | mail = {{MailingListsFor|Galaxy}} | ||
| logo_info = | | logo_info = | ||
| dev_ppl = | | 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. | ||
| dev_status = | | dev_status = | ||
| contact_email = | | contact_email = | ||
| − | | | + | [mailto:clements@galaxyproject.org Dave Clements] or [mailto:outreach@galaxyproject.org 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 = | | see_also = | ||
| − | | | + | | demo_server = http://usegalaxy.org/ |
| − | + | <!-- A full fledged, fully supported instance | |
| − | | | + | https://test.g2.bx.psu.edu/ |
| + | Test instance --> | ||
| + | | survey_link = Galaxy | ||
}} | }} | ||
Revision as of 00:38, 21 February 2013
{{ {{{template}}} | name = Galaxy | full_name = | status = release | 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
The 2013 Galaxy Community Conference (GCC2013) will be held June 30 through July 2 at the University of Oslo in Oslo, Norway. GCC2013 will feature 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.
GCC2012 was held in Chicago had over 200 attendees. Slides and videos of all talks at GCC2012 and GCC2011 are available on the Galaxy wiki.
| screenshot =
| 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 =
- General Galaxy info
- User documentation
- Source code documentation
- Search the whole universe of Galaxy docs
| 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 Learning Hub
- A wealth of training materials, including:
- Galaxy Tutorial
- As taught at the 2012 GMOD Summer School
| 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 }}
