Contents • Introduction • Linux User Interfaces • Linux File System • Linux Terminal Demonstration Introduction Linux • Unix-like operating system • GNU/Linux ⚫ GNU system packages with Linux Kernel
• Standard operating system for HPC / Servers / etc.
• Community driven, open-source and free to use and distribute • Thus, many flavors or distributions Linux Advantages & Disadvantages • Advantages ⚫ Free to use and distribute
⚫ Bugs are found and fixed quicker
⚫ Transparency natural fit for scientists
• Disadvantages ⚫ Software compilation – not user friendly
⚫ Not Windows Linux Distributions • Linux Mint (https://linuxmint.com/)
• Hanna Montana Linux (http://hannahmontana.sourceforge.net/)
Linux User Interfaces Linux User Interfaces • Two main types ⚫ Graphical User Interface (GUI)
⚫ Text Interface (Terminal)
• Main HPC interface → Text Interface
Linux GUIs • Many options • Desktop Managers ⚫ GNOME
⚫ KDE Plasma
⚫ XFCE
⚫ Cinnamon
⚫ ETC Linux Mint with Cinnamon Garuda Linux with KDE Plasma Rocky Linux with GNOME3 Terminal – Terminal Emulators Linux File System Linux File system • File System ⚫ Collection of methods OS uses to manage data on a storage device such as hard disks • Partition Types: ⚫ NTFS, FATx (Microsoft) ⚫ Ext4 (Linux) ⚫ HFS (Apple) • Windows can only read NTFS and FATx partition / not Ext4 • Linux can read most partition types • Files and directories organized differently from Windows Windows File System Windows File System Linux File system • All storage devices amalgamated into one root file system • Top directory --> Root or / • Storage devices mounted in directories within / • Home directories --> / home / <username> ⚫ Users have full permissions in their own home directories ⚫ No write permissions in system directories ⚫ More secure • File extensions for your convenience and not important in Linux Linux File system Linux File system Linux File system File and directory paths
Windows Linux
I: \ Fantasy /media/leon/MOVIES/Fantasy
Drive Directory Directory mount point Directory
Letter Linux Terminal Demonstration Introduction • Use terminal commands to navigate and perform actions • Each terminal command is usually a stand-alone program • Common interfaces with most CLI commands / programs ⚫ Positional arguments: cp <source> <destination> ⚫ Options/Flags can be in long form or short hand ⚫ Long form: --help ⚫ Short hand: -h ⚫ Using (-h) or (--help) --> most cases --> show how to use command/program ⚫ Using man <command> will display the command’s manual Navigation in the Linux • Short-cuts: ⚫ / : Root Directory ⚫ . : Present Working Directory (PWD) ⚫ .. : One directory above the PWD ⚫ ~ : Home directory for the current user ⚫ - : Previous directory (only used with cd) • pwd • ls • cd • find Performing File Operations • mkdir
• touch
• cp
• mv
• rm Viewing File Contents • cat
• more
• less
• head
• tail Miscellaneous Commands • tar
• screen Regular Expressions • Patterns that match strings
• Can become complex very quickly → gentle introduction
• Steps for crafting a regular expression:
• Identify common patterns
• Write the regular expression based on common pattern
• Test the regular expression
Identifying Patterns • Example: The following files are generated by an experiment: • foo_stats.txt • foo_seq1.fasta • foo_seq2.fasta • foo_seq3.fasta • foo_timings.fasta • hpc_job.error • hpc_job.output • hpc_job.nodes • hpc_job.txt Regular Expressions • Example: The following files are generated by an experiment: • foo_stats.txt • foo_seq1.fasta • foo_seq2.fasta • foo_seq3.fasta • foo_timings.fasta • hpc_job.error • hpc_job.output • hpc_job.nodes • hpc_job.txt Regular Expressions • Example: The following files are generated by an experiment: • foo_stats.txt • foo_seq1.fasta • foo_seq2.fasta • foo_seq3.fasta • foo_timings.fasta • hpc_job.error • hpc_job.output • hpc_job.nodes • hpc_job.txt Regular Expressions • Example: The following files are generated by an experiment: • foo_stats.txt • foo_seq1.fasta • foo_seq2.fasta • foo_seq3.fasta • foo_timings.fasta • hpc_job.error • hpc_job.output • hpc_job.nodes • hpc_job.txt Writing regular expressions Element Definition Example Character set or class Characters retaining their The prefix foo literal meaning Modifiers Expand or narrow the Asterisk (*) expands text to match selection to all characters Anchors Indicates the location Caret (^) indicates that from where to match the pattern should be at the beginning of the text
* Note that Anchors can only be used with tools such as grep and sed Writing regular expressions - Example • List all files that start with the prefix foo
• $ ls foo*
• List all files that end with the .fasta extension
• $ ls *.fasta
• Copy all files that start with the prefix hpc_job
