UAB Galaxy Workshop Tutorial: Difference between revisions
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= | = 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. | 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 [[media: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)] | |||
There are a number of options to | == Galaxy Data Import == | ||
* Uploading through the browser (http) | |||
* Copying files to cheaha and linking them in ( | There are a number of options to upload data: | ||
* Uploading through the browser (http) '''!!Max 2G file size!!''' | |||
* Copying files to cheaha and linking them in (sftp and scp) | |||
* Linking to an existing data library | * Linking to an existing data library | ||
An explanation of the tradeoffs can be found in this mini tutorial on [http://projects.uabgrid.uab.edu/galaxy/wiki/UploadingFiles uploading files] | An explanation of the tradeoffs can be found in this mini tutorial on [http://projects.uabgrid.uab.edu/galaxy/wiki/UploadingFiles uploading files]. | ||
= [[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. | |||
Go to [[Galaxy DNA-Seq Tutorial]] wiki page. | |||
Presentation [[media:RCD2011_DNA-Seq_Workshop_Talk.pdf|PDF]] or original [ftp://ftp.genome.uab.edu/ICS/Galaxy_RNAseq_tutorial/RCD2011%20DNA-Seq%20Workshop%20Talk.pptx PPTX]. | |||
For the purpose of realism, simplicity and speed, this tutorial uses a portion of a real | |||
= [[UAB_Galaxy_RNA_Seq_Step_by_Step_Tutorial|Galaxy RNA-Seq Tutorial]] = | |||
For the purpose of realism, simplicity and speed, this tutorial uses a small portion of a real mouse dataset that has kindly been provided by Dr. Kim Keeling. Our object is to determine gene expression differences between the control cells and the drugged cells. | |||
Go to [[UAB_Galaxy_RNA_Seq_Step_by_Step_Tutorial|Galaxy RNA-Seq Tutorial]]. | |||
= [[Galaxy Workflow Tutorial]] = | |||
This will cover use and creation of galaxy workflows. | 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. | This will cover topics such as doing galaxy development with git, customizing galaxy and running a personal instance of galaxy on cheaha. | ||
Latest revision as of 08:15, 16 September 2011
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 upload data:
- Uploading through the browser (http) !!Max 2G file size!!
- Copying files to cheaha and linking them in (sftp and scp)
- Linking to an existing data library
An explanation of the tradeoffs can be found in this mini tutorial on uploading files.
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.
Go to Galaxy DNA-Seq Tutorial wiki page.
Presentation PDF or original PPTX.
Galaxy RNA-Seq Tutorial
For the purpose of realism, simplicity and speed, this tutorial uses a small portion of a real mouse dataset that has kindly been provided by Dr. Kim Keeling. Our object is to determine gene expression differences between the control cells and the drugged cells.
Go to 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.