![Page 1: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/1.jpg)
Introduction to Galaxy at!UF HPC!
!Oleksandr Moskalenko!
Assoc. Sci., UF HPC Center!Biological Applications Support!
Matt Gitzendanner!Assoc Sci., Biology/HPC Training!
!
UF Research Computing
UF Research Computing Day 2011!
![Page 2: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/2.jpg)
Today’s research computing
![Page 3: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/3.jpg)
Approaches
![Page 4: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/4.jpg)
Approaches
![Page 5: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/5.jpg)
Approaches
![Page 6: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/6.jpg)
Approaches
![Page 7: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/7.jpg)
Command Line Environment
Login to head node!
Head node!
Interactive session or batch
submission!
Scheduler!
Your job runs on the
cluster!
Computing!resources!
![Page 8: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/8.jpg)
What is Galaxy?
![Page 9: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/9.jpg)
What is Galaxy?
✦ Computational biology platform!• Open and Web-based!• Accessible!• Reproducible!• Transparent!
![Page 10: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/10.jpg)
Galaxy Analysis Workspace
![Page 11: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/11.jpg)
Galaxy Analysis Workspace
![Page 12: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/12.jpg)
Galaxy Analysis Workspace
![Page 13: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/13.jpg)
Galaxy Analysis Workspace
![Page 14: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/14.jpg)
Galaxy Analysis Workspace
![Page 15: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/15.jpg)
Metadata
![Page 16: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/16.jpg)
Getting Data into Galaxy ✦ Upload a file from your computer!
• scp to HPC and load from within Galaxy!• Copy files to HPC using Samba!
✦ External data!• UCSC table
browser!• Biomart!• interMine /
modMine!
• EuPathDB !• EncodeDB!• EpiGRAPH!• FlyMine!• GrameneMart…!
![Page 17: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/17.jpg)
Data libraries
![Page 18: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/18.jpg)
Data Access Control
![Page 19: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/19.jpg)
Galaxy Tool Suites ✦ Text Manipulation!✦ Format Converters!✦ Filtering and Sorting!✦ Join, Subtract, Group !✦ Sequence Tools!✦ Multi-species
Alignment Tools!✦ Genomic Interval
Operation!
✦ Summary Statistics, graphing!
✦ Regional Variation!✦ EMBOSS!✦ Evolution/Phylogeny!✦ RNA-Seq!✦ ChIP-Seq!✦ GATK !
![Page 20: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/20.jpg)
A galaxy of tools
![Page 21: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/21.jpg)
Galaxy Workflows
![Page 22: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/22.jpg)
Galaxy Workflows
![Page 23: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/23.jpg)
Galaxy Workflows
![Page 24: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/24.jpg)
Visualization
![Page 25: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/25.jpg)
Sharing and publishing
![Page 26: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/26.jpg)
Sharing and publishing
![Page 27: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/27.jpg)
Sharing and publishing
![Page 28: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/28.jpg)
Galaxy pages
![Page 29: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/29.jpg)
Summary ✦ Analyze data without the CLI !✦ Visualize the results!✦ Publish histories, workflows, and
annotated pages!✦ Add new tools, get support @ HPC!✦ Focus on your science, not minutiae!✦ UF Galaxy – coming to a browser
near you!!
![Page 30: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/30.jpg)
Demo
![Page 31: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/31.jpg)
MACS demo
http://galaxy.hpc.ufl.edu!
![Page 32: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/32.jpg)
MACS demo
http://galaxy.hpc.ufl.edu!
![Page 33: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/33.jpg)
History/Shared Data
http://galaxy.hpc.ufl.edu!
![Page 34: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/34.jpg)
Shared Data
![Page 35: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/35.jpg)
MACS – Load data
![Page 36: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/36.jpg)
What’s inside
![Page 37: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/37.jpg)
MACS (NGS: Peak Calling)
![Page 38: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/38.jpg)
Submission form
![Page 39: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/39.jpg)
MACS options
• Basic:!• Treatment file: Your alignment file – choose BAM file!
• Effective genome size: Human (hg19) – must set once!
• Advanced:!• Use model or shift size!
• Model - fold enrichment (small and large): 10:30!
• Bandwidth – scan bandwidth size for model or ½ window size without the model: default is 300!
![Page 40: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/40.jpg)
Submit the job to cluster
![Page 41: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/41.jpg)
Cluster job run
![Page 42: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/42.jpg)
Job completion
![Page 43: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/43.jpg)
Build a genome browser track
![Page 44: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/44.jpg)
Submit a track build job
![Page 45: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/45.jpg)
Open the track
![Page 46: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/46.jpg)
Genome Browser
![Page 47: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/47.jpg)
Add a custom track
![Page 48: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/48.jpg)
Paste track data
![Page 49: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/49.jpg)
View track
![Page 50: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/50.jpg)
Zoom in, pan, etc.
![Page 51: UF Research Computing - Information Technology · PDF fileIntroduction to Galaxy at! UF HPC!! Oleksandr Moskalenko! Assoc. Sci., UF HPC Center! Biological Applications Support! Matt](https://reader037.vdocument.in/reader037/viewer/2022103011/5a7650ca7f8b9a63638d3066/html5/thumbnails/51.jpg)
• http://wiki.hpc.ufl.edu !• https://fisher.bioinformatics.ufl.edu!• http://hpc.ufl.edu/support!
- Frequently Asked Questions!
- Account set up and maintenance!
- Problem report submission!
- [email protected] - Biological applications support!
- [email protected] - Training!
Thank you!