UAB Galaxy Workshop Tutorial: Difference between revisions
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Time is limited, but this tutorial will account creation and logging in to galaxy and the cheaha cluster. This will be followed by a short but important section of how to get your data into galaxy and then finally tutorials on 2 common tasks: DNA-Seq and RNA-Seq. If there is time there will be an advanced section on workflow creation, Galaxy development and running your own personal galaxy instance. | Time is limited, but this tutorial will account creation and logging in to galaxy and the cheaha cluster. This will be followed by a short but important section of how to get your data into galaxy and then finally tutorials on 2 common tasks: DNA-Seq and RNA-Seq. If there is time there will be an advanced section on workflow creation, Galaxy development and running your own personal galaxy instance. | ||
=== Getting Started Tutorial === | |||
RCD 2011 Welcome to Galaxy Tutorial [[RCD 2011 Welcome to Galaxy tutorial.pdf|PDF]] or [ftp://ftp.genome.uab.edu/ICS/Galaxy_RNAseq_tutorial/RCD%202011%20Welcome%20to%20Galaxy%20tutorial.pptx PPTX (animations)] | |||
=== Galaxy Data Import === | === Galaxy Data Import === | ||
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An explanation of the tradeoffs can be found in this mini tutorial on [http://projects.uabgrid.uab.edu/galaxy/wiki/UploadingFiles uploading files]. For this tutorial we will be linking in a [http://projects.uabgrid.uab.edu/galaxy/wiki/DataLibraries data library] that has already been uploaded. | An explanation of the tradeoffs can be found in this mini tutorial on [http://projects.uabgrid.uab.edu/galaxy/wiki/UploadingFiles uploading files]. For this tutorial we will be linking in a [http://projects.uabgrid.uab.edu/galaxy/wiki/DataLibraries data library] that has already been uploaded. | ||
== [[Galaxy DNA-Seq Tutorial]] == | == [[Galaxy DNA-Seq Tutorial]] == | ||
Revision as of 21:21, 15 September 2011
UAB Galaxy Tutorial
Overview
Time is limited, but this tutorial will account creation and logging in to galaxy and the cheaha cluster. This will be followed by a short but important section of how to get your data into galaxy and then finally tutorials on 2 common tasks: DNA-Seq and RNA-Seq. If there is time there will be an advanced section on workflow creation, Galaxy development and running your own personal galaxy instance.
Getting Started Tutorial
RCD 2011 Welcome to Galaxy Tutorial PDF or PPTX (animations)
Galaxy Data Import
There are a number of options to UploadLargeData.
- Uploading through the browser (http)
- Copying files to cheaha and linking them in (ftp and scp)
- Linking to an existing data library
An explanation of the tradeoffs can be found in this mini tutorial on uploading files. For this tutorial we will be linking in a data library that has already been uploaded.
Galaxy DNA-Seq Tutorial
For the purpose of realism, simplicity and speed, this tutorial uses a portion of a real virus dataset that has kindly been provided by Dr. Mark Prichard and was one of the first NextGen sequencing projects undertaken by CCTS. Our object is to process the results from 2 viruses, a wild type Vaccinia virus and a derived mutant strain and analyze the differences in Galaxy.
Galaxy RNA-Seq Tutorial
Galaxy Workflow Tutorial
This will cover use and creation of galaxy workflows.
Galaxy Advanced Topics
This will cover topics such as doing galaxy development with git, customizing galaxy and running a personal instance of galaxy on cheaha.