Galaxy - Revision history

Mhanby@uab.edu: /* Support */

2017-12-13T14:48:29Z

Support

← Older revision		Revision as of 14:48, 13 December 2017
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	== Support ==		== Support ==
	UAB galaxy-users list-serv: [~~http~~://~~vo.uabgrid~~.uab.edu/~~sympa/subscribe~~/~~galaxy~~-~~user~~ subscribe] [https://~~vo.uabgrid~~.uab.edu/~~sympa/arc~~/~~galaxy~~-~~user~~ search].		UAB galaxy-users list-serv: [https://listserv.uab.edu/scgi-bin/wa?SUBED1=GALAXY-HELP&A=1 subscribe] [https://listserv.uab.edu/scgi-bin/wa?SUBED1=GALAXY-HELP&A=1 search].

	UAB galaxy-help list-serv: [mailto:galaxy-help@~~vo.uabgrid~~.uab.edu] to contact admins of the UAB galaxy instance.		UAB galaxy-help list-serv: [mailto:galaxy-help@listserv.uab.edu] to contact admins of the UAB galaxy instance.

	== Privacy ==		== Privacy ==

Curtish@uab.edu: /* Galaxy@UAB */

2013-03-11T18:12:33Z

Galaxy@UAB

← Older revision		Revision as of 18:12, 11 March 2013
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	The UAB Galaxy instance can be accessed at https://galaxy.uabgrid.uab.edu using BlazerID credentials. No account on the cluster is needed.		The UAB Galaxy instance can be accessed at https://galaxy.uabgrid.uab.edu using BlazerID credentials. No account on the cluster is needed.
	However, the tools installed for galaxy (BWA, etc) can be accessed via the command line if you have an account on the cluster.		However, the tools installed for galaxy (BWA, etc) can be accessed via the command line if you have an account on the cluster.

			== Loading Data ==
			See [[Galaxy_File_Uploads]].

	== Available Tools ==		== Available Tools ==
	Following is a partial list highlighting some of the important tools available. Additional tools can be installed upon request. To search for tools already integrated into the Galaxy system, see the [http://toolshed.g2.bx.psu.edu/ Galaxy ToolShed].		Following is a partial list highlighting some of the important tools available. Additional tools can be installed upon request. To search for tools already integrated into the Galaxy system, see the [http://toolshed.g2.bx.psu.edu/ Galaxy ToolShed].

Curtish@uab.edu: /* Installed Genome Indexes */ added additional genomes hg16 hg17 mm8 mm7 mm6 mm5, mostly for liftOver support.

2013-03-11T18:11:16Z

Installed Genome Indexes: added additional genomes hg16 hg17 mm8 mm7 mm6 mm5, mostly for liftOver support.

← Older revision		Revision as of 18:11, 11 March 2013
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	\|+		\|+
	! dbkey !! Genome !! Accessions		! dbkey !! Genome !! Accessions
			\|-
			\| hg19 \|\| Human Feb. 2009 (GRCh37/hg19) (hg19)
			\|-
			\| hg18 \|\| Human Mar. 2006 (NCBI36/hg18) (hg18)
			\|-
			\| hg17 \|\| Human May 2004 (NCBI35/hg17) (hg17)
			\|-
			\| hg16 \|\| Human July 2003 (NCBI34/hg16) (hg16)
			\|-
			\| mm10 \|\| Mouse Dec. 2011 (GRCm38/mm10) (mm10)
	\|-		\|-
	\| mm9 \|\| Mouse July 2007 (NCBI37/mm9) (mm9)		\| mm9 \|\| Mouse July 2007 (NCBI37/mm9) (mm9)
	\|-		\|-
	\| ~~mm10~~ \|\| Mouse ~~Dec~~. ~~2011~~ (~~GRCm38~~/~~mm10~~) (~~mm10~~)		\| mm8 \|\| Mouse Feb. 2006 (NCBI36/mm8) (mm8)
	\|-		\|-
	\| ~~hg18~~ \|\| ~~Human Mar~~. ~~2006~~ (~~NCBI36~~/~~hg18~~) (~~hg18~~)		\| mm7 \|\| Mouse Aug. 2005 (NCBI35/mm7) (mm7)
	\|-		\|-
	\| ~~hg19 \|\| Human Feb. 2009 (GRCh37/hg19) (hg19)~~		\| mm6
	\|-		\|-
	\|~~sacCer2 \|\| S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2)~~		\| mm5
	\|-		\|-
	\|sacCer3 \|\| S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)		\|sacCer3 \|\| S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)
			\|-
			\|sacCer2 \|\| S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2)
	\|-		\|-
	\|ce10 \|\| C. elegans Oct. 2010 (WS220/ce10) (ce10)		\|ce10 \|\| C. elegans Oct. 2010 (WS220/ce10) (ce10)
			\|-
			\|rn5 \|\| Rat Mar. 2012 (RGSC 5.0/rn5) (rn5)
	\|-		\|-
	\|rn4 \|\| Rat Nov. 2004 (Baylor 3.4/rn4) (rn4)		\|rn4 \|\| Rat Nov. 2004 (Baylor 3.4/rn4) (rn4)
	\|-
	~~\|rn5 \|\| Rat Mar. 2012 (RGSC 5.0/rn5) (rn5)~~
	\|-		\|-
	\|danRer7 \|\| Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7)		\|danRer7 \|\| Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7)

Curtish@uab.edu: /* Overview */

2013-03-11T18:05:59Z

Overview

← Older revision		Revision as of 18:05, 11 March 2013
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	= Overview =		= Overview =
	The UAB Galaxy platform for experimental biology and comparative genomics designed to help you analyze multiple alignments, compare genomic annotations, profile metagenomic samples and more from your web browser. This platform is built on [http://main.g2.bx.psu.edu/ Galaxy], backed by the [http://docs.uabgrid.uab.edu/wiki/Cheaha Cheaha compute cluster], and powered by [http://uabgrid.uab.edu/ UABgrid].		The UAB Galaxy platform for experimental biology and comparative genomics is designed to help you analyze multiple alignments, compare genomic annotations, profile metagenomic samples and more from your web browser. This platform is built on [http://main.g2.bx.psu.edu/ Galaxy], backed by the [http://docs.uabgrid.uab.edu/wiki/Cheaha Cheaha compute cluster], and powered by [http://uabgrid.uab.edu/ UABgrid].

	The primary uses of UAB Galaxy are to provide a simple web interface for NGS (short read sequencing) analysis for genomic and transcriptomic datasets, using tools like BWA, Bowtie, Tophat and Cufflinks, as well as simple sequence manipulation via the EMBOSS toolkit.		The primary uses of UAB Galaxy are to provide a simple web interface for NGS (short read sequencing) analysis for genomic and transcriptomic datasets, using tools like BWA, Bowtie, Tophat and Cufflinks, as well as simple sequence manipulation via the EMBOSS toolkit.
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	== Privacy ==		== Privacy ==

	Note that your data will be stored on the cluster filesystem, and while not accessible to ordinary users, it can be easily accessed by any of the galaxy or cluster administrators. It is not encrypted. Do not store sensitive information in this system.		Note that your data will be stored on the cluster filesystem, and while not accessible to ordinary users, it can be easily accessed by any of the galaxy or cluster administrators. It is not encrypted. Do not store sensitive information in this system.

	= Galaxy@UAB =		= Galaxy@UAB =

Curtish@uab.edu: /* Available Tools */

2013-03-07T21:10:32Z

Available Tools

← Older revision		Revision as of 21:10, 7 March 2013
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	! bowtie		! bowtie
	\| 0.12.7 \|\| Align genomic short reads to a reference genome		\| 0.12.7 \|\| Align genomic short reads to a reference genome
			\|-
			! tophat
			\| 1.4.0 \|\| Align transcriptome short reads to a reference genome
			\|-
			! cufflinks, cuffdiff, cuffcompare
			\| 1.3.0 \|\| Reconstruct and quantify transcript levels from tophat alignments.
	\|-		\|-
	! samtools		! samtools
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	! velvet		! velvet
	\| 1.1.03 \|\| Denovo Assembly		\| 1.1.03 \|\| Denovo Assembly
	\|-
	~~! Top Hat~~
	~~\| 1.4.0 \|\| Align transcriptome short reads to a reference genome~~
	\|-
	~~! Cuff Links~~
	~~\| 1.3.0 \|\| Reconstruct and quantify transcript levels from tophat alignments.~~
	\|-		\|-
	! [http://en.wikipedia.org/wiki/EMBOSS EMBOSS]		! [http://en.wikipedia.org/wiki/EMBOSS EMBOSS]
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	\|-		\|-
	\|}		\|}


	== Installed Genome Indexes ==		== Installed Genome Indexes ==

Curtish@uab.edu: /* Organisms */

2013-03-07T21:08:58Z

Organisms

Show changes

Curtish@uab.edu: /* microbes */

2013-03-07T21:08:37Z

microbes

Show changes

Curtish@uab.edu: add available-genomes list from galaxy data-cache

2013-03-07T20:59:52Z

add available-genomes list from galaxy data-cache

Show changes

Curtish@uab.edu: /* Galaxy@UAB */ add list of available genomes, update and abbreviate software list

2013-03-07T20:30:39Z

Galaxy@UAB: add list of available genomes, update and abbreviate software list

Show changes

Curtish@uab.edu: /* Overview */

2013-03-07T19:28:54Z

Overview

← Older revision		Revision as of 19:28, 7 March 2013
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	= Overview =		= Overview =
	The UAB Galaxy platform for experimental biology and comparative genomics designed to help you analyze multiple alignments, compare genomic annotations, profile metagenomic samples and more from your web browser. This platform is built on [http://main.g2.bx.psu.edu/ Galaxy], backed by the [http://docs.uabgrid.uab.edu/wiki/Cheaha Cheaha compute cluster], and powered by [http://uabgrid.uab.edu/ UABgrid]. ~~Documentation on the~~ UAB ~~installation can be found on~~ the ~~[http://docs.uabgrid.uab.edu/wiki/Galaxy UAB Galaxy wiki]~~.		The UAB Galaxy platform for experimental biology and comparative genomics designed to help you analyze multiple alignments, compare genomic annotations, profile metagenomic samples and more from your web browser. This platform is built on [http://main.g2.bx.psu.edu/ Galaxy], backed by the [http://docs.uabgrid.uab.edu/wiki/Cheaha Cheaha compute cluster], and powered by [http://uabgrid.uab.edu/ UABgrid].

			The primary uses of UAB Galaxy are to provide a simple web interface for NGS (short read sequencing) analysis for genomic and transcriptomic datasets, using tools like BWA, Bowtie, Tophat and Cufflinks, as well as simple sequence manipulation via the EMBOSS toolkit.

	== Using Galaxy / [[UAB Galaxy Workshop Tutorial\|Tutorials]] ==		== Using Galaxy / [[UAB Galaxy Workshop Tutorial\|Tutorials]] ==

	There are ~~several~~ [~~[UAB Galaxy Workshop Tutorial\|UAB~~ tutorials ~~on NGS Analysis with Galaxy~~]~~], created for~~ [~~[2011_HPC_Boot_Camp\|HPC Boot Camp 2011~~]~~] and a nice talk by Jeremy Goecks during [[2011\|Research Computing Day 2011~~.]]		There are numerous [http://wiki.g2.bx.psu.edu/Learn/Screencasts general tutorials] online at the [http://main.g2.bx.psu.edu/ Penn State public Galaxy site] that are worth looking at.

	There are also ~~numerous~~ [~~http://wiki.g2.bx.psu.edu/Learn/Screencasts general~~ tutorials] ~~online at the~~ [~~http://main~~.~~g2.bx.psu.edu/ Penn State public Galaxy site~~] ~~that are worth looking at.~~		There are also several [[UAB Galaxy Workshop Tutorial\|UAB tutorials on NGS Analysis with Galaxy]], created for [[2011_HPC_Boot_Camp\|HPC Boot Camp 2011]] and a nice talk by Jeremy Goecks during [[2011\|Research Computing Day 2011.]]

	= Galaxy@UAB =		= Galaxy@UAB =