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Tutorial: Welcome to Galaxy

Tutorial: Welcome to Galaxy. Research Computing Workshop 2011 Curtis Hendrickson (curtish@uab.edu) CCTS Biomedical Informatics Service. What is Galaxy?. Open source web application for data analysis Command-line free cluster integration Multi- Tera byte “scratch” storage in UAB cloud

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Tutorial: Welcome to Galaxy

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  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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