Course Topic Reference Index
- Why use linux
- Looking and moving around: ls, cd
- Creating, copying, moving, and deleting files
- Looking at file contents: cat, less, tail, head
- More commands: pwd, gzip, tar, chmod
- Moving files between systems: scp, rsync
- Other commands: man, which, echo, history
- Text editing with VIM
INTRODUCTION TO HIGH PERFORMANCE COMPUTING
- Basic HPC architecture
- Environment variables: env, echo, export
- Modules
- The .bashrc
- Batch job submission
- Viewing text files: cat, head, tail, less
- Data formats: FASTA, FASTQ, BED, GFF3
- Filtering text files: cut, grep, uniq
- Redirecting and piping
- Manipulating files: paste, sort, diff, sed, awk
- Application: example sequence analysis pipeline
HPC SOFTWARE ENVIROMENT INTRODUCTION
- Lonestar 5: specs, file system, compilers
- Installing an application
- Testing an application
- Profiling an application
- Sharing an application
- Making modules
DATA MANAGEMENT AND COLLABORATION
- Why do we need data management
- How is data organized
- TACC disk/file system
- How to use disk resources: active vs inactive
- File information: du, df, quota
- Data clean up, compressing, archiving
- Moving data off site or to tape
- Best practices
- Duplication
- Background - Protein Blast
- Automating workflows: arguments, conditionals
- Automating workflows: data parallelism
- Transcriptome analysis