Todays research computing UF Research Computing Introduction to - PDF document

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6/20/12 Todays research computing UF Research Computing Introduction to Galaxy at UF HPC Matt Gitzendanner Oleksandr Moskalenko Approaches Different approaches, same result Head node Scheduler Computing

6/20/12 � Today’s research computing UF Research Computing Introduction to Galaxy at � UF HPC � � Matt Gitzendanner � � Oleksandr Moskalenko � Approaches Different approaches, same result Head node � Scheduler � Computing � resources � Interactive session or batch Your job submission � runs on the cluster � What is Galaxy? What is Galaxy? Galaxy Provides Life Support for ✦ Computational biology platform � NGS Exploration � • Open and Web-based � • Accessible � • Reproducible � • Transparent � 1 �
6/20/12 � Galaxy Analysis Workspace Galaxy Analysis Workspace Galaxy Analysis Workspace Galaxy Analysis Workspace Galaxy Analysis Workspace Metadata 2 �
6/20/12 � Getting Data into Galaxy Data libraries ✦ Upload a file from your computer � • scp or copy files to HPC � • Load from within Galaxy � - http://wiki.hpc.ufl.edu/index.php/Galaxy_Data_Import � ✦ External data � • UCSC table • EuPathDB � • EncodeDB � browser � • Biomart � • EpiGRAPH � • interMine / • FlyMine � • GrameneMart… � modMine � Data Access Control Galaxy Tool Suites ✦ Text Manipulation � ✦ Summary Statistics, graphing � ✦ Format Converters � ✦ Regional Variation � ✦ Filtering and Sorting � ✦ EMBOSS � ✦ Join, Subtract, Group � ✦ Evolution � ✦ Sequence Tools � ✦ RNA-Seq � ✦ Multi-species Alignment Tools � ✦ ChIP-Seq � ✦ Genomic Interval ✦ GATK � Operation � ✦ Phylogenetics ??? � A galaxy of tools Galaxy Workflows 3 �
6/20/12 � Galaxy Workflows Galaxy Workflows Visualization Sharing and publishing Sharing and publishing Sharing and publishing 4 �
6/20/12 � Galaxy pages You can setup analyses on datasets that will be produced by running jobs. They will be queued and will run once the dataset becomes available. � Summary How to get help ✦ Analyze data without the CLI � ✦ Asking for help � ✦ Visualize the results � • Support Request Tickets � ✦ Publish histories, workflows, and - http://support.hpc.ufl.edu � annotated pages � - Use for everything - not just software bugs but for any questions or help requests � ✦ Add new tools, get support @ HPC � - Searchable database of solutions � • When you don’t have access to web � ✦ Focus on your science, not minutiae � - support@hpc.ufl.edu � ✦ UF Galaxy – coming to a browser - om@hpc.ufl.edu (Biological Support) near you! � - magitz@ufl.edu (Bio training and Q/A) � Documentation ✦ UF HPC Encyclopedia � Thank • http://wiki.hpc.ufl.edu � - Documents on hardware and software resources � - User guides � - Sample submission scripts � you! � - Research-specific sections � • http://hpc.ufl.edu/support � - Frequently Asked Questions � - Account set up and maintenance � 5 �

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