I2rda Course Cheatsheet

Ways of getting out of things

• Typing exit (the terminal, command-line, queue system, screen program)
• Ctrl+C, usually interrupts a process
• q()in R.
• q in less and xpdf
• alt-F4, sometimes for R plots for instance.
• Ctrl+W, to close a tab.

the module software loading program

• moduleav to see what's available
• moduleav |grep samtools to see only those lines containing samtools
• module help samtools, to see any possible help information (samtools in this case) on the module (not always informative).
• module list to see your currently loaded software modules
• module load samtools to load a certain (samtools in this case) module (Default modules do not need version numbers).
• module unload samtools to unload a certain (samtools in this case) module (Default modules do not need version numbers).

GNU screen program

• type screen to get in.
• type exit to get out of your screen sessions
• ctrl+l, n: cycle through screen windows
• ctrl+l, :hardcopy RET: create a file with a copy of all inputs and outputs of your session.
• ctrl+l,d: detach screen session
• type screen -r to recover a detached session.
• ctrl+l,K: abandon current session. It will be lost.
• ctrl+l,ESC: enter scroll or copy mode. PgUp an PgDn will now work. Esc to get out.

Graphical programs

• Note Using graphical programs on the cluster is slow, because very many pixels all have to be sent down the network.
• to view pdf files: xpdf <file.pdf>.q will exit.
• to view spreadsheet, tsv or csv files: gnumeric <file.csv>. Alt-F4 to get out.
• When R pops up a plot, Alt-F4 to get out.

Command-line Navigation

• ctrl + a: go to beginning of line
• ctrl + d: delete a character (useful when used after above)
• ctrl + e: go to end of line
• ctrl + w: delete current word backwards, word behind if in space
• ctrl + y: yank, or paste most recent deletion (useful when used after above to repeat deletion)
• ctrl + /: undo changes
• ctrl + x, <BACKSPACE>: search backwards for a character, here?
• ctrl + r, ?: search backwards for a character, here?
• alt + b: move backwards word-wise.
• alt + f: move backwards word-wise
• alt + d: delete current word forwards, next word if in space
• ctrl + k: delete to end of line

Pagers: man, less and vim keys

• q, to get out again.
• gg, for top of the page
• G, for bottom of page
• Ctrl+f, to advance one page forward.
• Ctrl+b, to move one page back.
• / to search, it allows you type in a search term at the bottom.
• The up,down,PgUp and PgDn keys all work as expected.

Linux shortcut symbols

• . the directory you are currently in, often used with mv, cp or ln -s to mean "in here please"
• .. the directory one level above the one you are currently in, aka. the parent directory

- To change directory to the one above your are in: cd ..

• To returns to the last directory you were working in before this one: cd –
• On its own, cd bring you to your home directory
• ~ shorthand for your home directory, where all your data is kept.
• > directs output of one command into a file
• | often called the pipe operator: directs output of one command into another command.

Keybindings for using the history file

• :<RET>: save command in history, do not execute.
• !$<RET>: the final argument of the last command
• !!<RET>: the entire last command
• !:1-$<RET>: everthing except the first word of the last command
• !$<RET>: the final argument of the last command
• ^then^now<RET>: replace the first occurence of then in last command with now
• !!:gs/then/now/<RET>: replace the ALL occurences of "then" in last command with "now"
• !!:gs/then/now/:p<RET>: as above except do not execute.

Using vim

• type vim to get in, and :q! to get out without saving.
• ZZ to save onto to current filename. ":sav fname" otherwise
• It opens in "normal" mode which is similar to less, in that direct editing is not expected.
• This is changed by pressing i. To get back to normal mode, press the ESC key.
• In normal mode u undoes any changes
• : while in normal mode allows command sto be entered
• Visual: enabled by "v" or "V" (visual block), sub-box at the bottom open.
• After v or V, movement keys ":%" will operate on whole document, ":’a,’b" operate between two marks, ":42,45" between two line numbers
• search via "/", ":set hlsearch" to see all the hits

Getting by in only normal mode

• movement keys, "w" jump via start of words; "e" jump via ends; "fc" jump to next c
• "0" for start of line, "A" for end of line and into insert mode
• "x" delete current character, "xp" switch positions of current and next character
• "yyp" copy current line and paste it underneath
• "dd" delete line, "2d" delete this and following two lines. "dgg" delete to start, "dG" delete to end
• "dw" delete current word
• Command: Activated by ":", sub-box at the bottom open, rich command language
• Visual: Activated by v or ctrl+v (visual block), sub-box at the bottom open, rich command language

Advanced but really useful commands

• :colorscheme desert change to the desert colour scheme, there are many others: morning, delek.
• :%s/snooze/sneeze/gc also works
• :g/sneeze/d delete all lines without sneeze"
• :v/sneeze/d delete all lines with sneeze"
• ":42y[RET]p" paste line 42
• "d214G" delete up to line 214
• "y214G" copy up to line 214
• :set list, all non-printing characters are also shown.
• :set hlsearch, will highlight all search occurrences.
• :set nu, show line numbers.

a fast pdf viewer: xpdf

• xpdf mypdffile.pdf opens mypdffile.pdf using the X11 graphical system
• q to get out
• + to maker bigger
• - to make smaller
• Spacebar for bottom of page
• n for next page
• p for previous page
• alt+f toggle for full screen and back

IGV Genome browser keys

• ctrl-R Defines the region currently in view as a region of interest.
• ctrl-F/ctrl-B Skip forward to the next feature and back to the last feature.
• ctrl-shift-F/ctrl-shift-B If you have the feature track expanded and have selected one of the rows, this will skip forward to the next exon or back to the last exon.
• alt-left/alt-right, move you back and forward through your IGV history.
• Arrow-keys Pans left, right, up, and down in the current chromosome.
• Home/End-keys Skips to the page top or bottom of the current view, then pages right or left respectively.
• PageUp/PageDown-keys Pages up and down the current view.