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This page should serve as a reference for the many "things Linux" we use in this course. It is by no means complete – Linux is **huge** – but offers introductions to many important topics.

Table of Contents

Terminal programs

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  • brackets ( [ ] ) to allow for any character in the list of characters between the brackets.
    • and you can use a hyphen ( - ) to specify a range of characters (e.g. [A-G])
  • braces ( {  } ) enclose a list of commancomma-separated substrings strings to match (e.g. {dog,pony})

For example:

  • ls *.bam – lists all files in the current directory that end in .bam
  • ls [A-Z]*.bam – does the same, but only if the first character of the file is a capital letter
  • ls [ABcd]*.bam – lists all .bam files whose 1st letter is A, B, c or d.
  • ls *.{fastq,fq}.gz – lists all .fastq.gz and .fq.gz files.

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  1. single quoting (e.g. 'some text') – this serves two purposes
    • it It groups together all text inside the quotes into a single argument that is passed to the command.
    • it It tells the shell not to "look inside" the quotes to perform any evaluations
      .
      • Anything any environment variables in the text – or anything that looks like an environment variable – are variable or a bash meta-character is not evaluated.
      • no No pathname globbing (e.g. *) is performed.
  2. double quoting (e.g. "some text") – also serves two purposes
    • it It groups together all text inside the quotes into a single argument that is passed to the command.
    • it It allows environment variable evaluation (but inhibits pathname globbing).
  3. backtick quoting (e.g. `date`)
    • It evaluates the expression inside the backticks.
    • the The resulting standard output of the expression replaces the backticked text.

Using Commands

Command options
Anchor
Command options
Command options

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  1. Single-letter short options, which start with a single dash ( - ) and can often be combined, like:

    Code Block
    languagebash
    titleExamples of different short options
    head -20 # show 1st 20 lines
ls -lhtS (equivalent to ls -l -h -t -S)


  2. Long options use the convention that double dashes ( -- ) precede the multi-character option name, and they can never be combined. Strictly speaking, long options should be separated from their values by the equals sign ( = ) according to the POSIX standard (see https://en.wikipedia.org/wiki/POSIX). But most programs let you use a space as separator also. Here's an example using the mira genome assembler:

    Code Block
    languagebash
    titleExample of long options
    mira --project=ct --job=denovo,genome,accurate,454 -SK:not=8


  3. Word options, illustrated in the GATK command line to call SNPs below.

    • Word options combine aspects of short and long options – they usually start with a single dash ( - ), but can be multiple letters and are never combined.

    • Sometimes the option (e.g. java's -Xms initial memory heap size option), and its value (512m which means 512 megabytes) may be smashed together.

    • Other times a multi-letter switch and its value are separated by a space (e.g. -glm BOTH).

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Notice that bwa, like many NGS programs, is written as a set of sub-commands. This top-level help displays the sub-commands available. You then type bwa <command> to see help for the sub-command:

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  • ls - list the contents of the specified directory
    • -l says produce a long listing (including file permissions, sizes, owner and group)
    • -a says show all files, even normally-hidden dot files whose names start with a period ( . )
    • -h says to show file sizes in human readable form (e.g. 12M instead of 12201749)
  • cd <whereto> - change the current working directory to <whereto>. Some special <wheretos>:
    •  .. (period, period) means "up one level"
    •  ~ (tilde) means "my home directory"
  • file <file> tells you what kind of file <file> is
  • df shows you the top level directory structure of the system you're working on, along with how much disk space is available
    • -h says to show sizes in human readable form (e.g. 12G instead of 12318201749)
  • pwd - display the present working directory
    • -P says to display the full absolute path

Create, rename, link to, delete files

  • touch <file> – create an empty file, or update the modification timestamp on an existing file
  • mkdir -p <dirname> – create directory <dirname>.  
    • -p says to create any needed subdirectories also
  • mv <file1> <file2> – renames <file1> to <file2>
    • mv <file1> <file2> ... <fileN> <dir><to_dir>/  – moves files <file1> <file2> ... <fileN> into directory <dir> <to_dir>
    • mv -t <to_dir> <file1> <file2> ... <fileN> – same as above but specifies the target directory as an option (-t <to_dir>).
  • ln -s <path> creates a symbolic (-s) link to <path> in the current directory
    • a symbolic link can be deleted without affecting the linked-to file
    • default link name corresponds to the last name component in <path>
    • always change into (cd) the directory where you want the link before executing ln -sa symbolic link can be deleted without affecting the linked-to file
  • rm <file> deletes a file. This is permanent - not a "trash can" deletion.
    • rm -rf  <dirname> deletes an entire directory – be careful!

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