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Introduction to Galaxy: A Workshop on Biomedical Data Analysis and Workflow Management

Join us for the 2011 Galaxy Research Computing Workshop led by Curtis Hendrickson at UAB. Learn about Galaxy, the open-source web application designed for data analysis and command-line-free cluster integration. This workshop covers multi-terabyte storage in UAB cloud, managing data workflows, and sharing protocols. We will focus on Next Generation Sequence analysis and explore EMBOSS tools, data upload methods, and handling large datasets. Ideal for those interested in improving their biomedical informatics skills.

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Introduction to Galaxy: A Workshop on Biomedical Data Analysis and Workflow Management

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Presentation Transcript

  1. Tutorial: Welcome to Galaxy Research Computing Workshop 2011 Curtis Hendrickson (curtish@uab.edu) CCTS Biomedical Informatics Service

  2. What is Galaxy? • Open source web application for data analysis • Command-line free cluster integration • Multi-Terabyte “scratch” storage in UAB cloud • Galaxy manages data and workflows/protocol • Allows sharing of data & protocols • Plug-ins for each tool, can add your own tools • Today, we will discuss using it for Next Generation Sequence analysis • Note that EMBOSS sequence analysis tools installed

  3. First Time Login • https://galaxy.uabgrid.uab.edu • Re-direction to BlazerID login

  4. Homepage Tools History

  5. 1. Name your history

  6. Get Data – Upload File

  7. Upload File from Desktopset format & genome!

  8. Upload File from Desktop transfer and decompress

  9. 3. Get Data – Shared Data Libraries

  10. 4. Get Data – http/ftp server (NOT HudsonAlpha)

  11. 5. Get Data – BIG FILES move to UAB cloud Get account on Cheaha cluster Secure Transfer: scp, SSH Secure File Transfer http://www.uab.edu/it/software Transfer to /lustre/scratch/user/projects_name Uncompress (/share/apps/galaxy/galaxy-tools/bin/q_gunzip) Get 10Gb network connection from IT! Desktop Cheaha

  12. 5. Get Data – BIG FILES Bring UAB cloud scratch files into Galaxy

  13. Get Data – UCSC Annotation PigF

  14. Get Data – UCSC Annotation

  15. Get Data – UCSC Annotation

  16. Get Data – UCSC Annotation Click Dataset “title” to see metadata Click Eyeball to show data

  17. Get Data – UCSC Annotation Click “pencil” to edit metadata Click “disk” to download

  18. Get Data – UCSC Annotation Eyeball of large data shows a sample

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