Andrew Severin

Andrew Severin

Andrew manages the Genome Informatics Facility at Iowa State University. His academic background is in biochemistry with a Ph.D. in Biophysics/NMR spectroscopy. He is an interdisciplinary scientist working at the interface of Genetics and Bioinformatics, translating Big Data into informative data for interesting biological questions. He is passionate about evolution and the science behind the genome.

DataScience Workbook / 06: High-Performance Computing (HPC) / 3. Setting up your home directory for data analysis / 3.1. Example .bashrc file configuration

Introduction

The .bashrc for bash shell is one of the most useful files for a unix user. It is read every time a new shell is created (for example when submitting jobs). In many HPC systems, the .bash_profile will also contain a line that will source the .bashrc upon login. Below is a .bashrc template that has examples of useful features you may want to include in your own .bashrc file, including:

  • Exports
  • Singularity
  • Aliases
  • Never ending history
  • Functions

How to set up .bashrc?

  1. Make a backup of your original .bashrc file. 
    cp .bashrc .bashrc.orig

  2. Copy the .bashrc file contained inside the code block below to a new .bashrc file.

  3. Update the following lines with the correct information. 
    export PROJECTFOLDER=/PATH/To/Working/Directory
alias gclone='git clone git clone git@github.com:GITHUBID/$1'  # update your gitorganization or ID here

example .bashrc

# /etc/skel/.bashrc
# Source global definitions

if [ -f /etc/bashrc ]; then
    . /etc/bashrc
fi

# Uncomment the following line if you don't like systemctl's auto-paging feature:
# export SYSTEMD_PAGER=

###############################
## Exports: When you need a variable every time you login.
###############################

# Extend your PATH to find locally installed programs or scripts
export PATH="~/bin:$PATH"
export PATH="$PATH:/home/$USER/.local/bin"

# corrects for Error:  E437: terminal capability "cm" required
export TERM=xterm

# Project Directory  -  be sure to update this path
export PROJECTFOLDER=/PATH/To/Working/Directory


###############################
## User defined Modules  -  this is where you might put modules you always load or modules you have installed yourself
###############################

# module load singularity

# Give others in your group read but (no write or execute) permissions upon file/folder creation
umask 0022


###############################
## Singularity
###############################

## Singularity Variables added to your path
if !  [ -d $PROJECTFOLDER/NXFContainers ]; then
    mkdir $PROJECTFOLDER/NXFContainers
fi
  export NXF_SINGULARITY_CACHEDIR=$PROJECTFOLDER/NXFContainers


###############################
## Aliases:  Make your most commonly used commands shorter!
###############################

  alias table='column  -t | less -S'  # this produces better columns for output cat file | table
  alias whitespace="sed 's/ /·/g;s/\t/￫/g;s/\r/§/g;s/$/¶/g'"  # show the whitespaces in a file

  alias pwd='pwd -P'                  # always show the full path and not softlinked path to folder

  # add color to grep and ls
  alias grep='grep --color=auto'
  alias fgrep='fgrep --color=auto'
  alias egrep='egrep --color=auto'
  alias ls='ls --color=auto -v'

  # File and folder size
  alias du='du -kh'                   # Makes a more readable output.
  alias df='df -kTh'
  alias dd='du -sch *'
  alias dG='du -hs * | awk '$1~"G"''  #show all files/folders with a size in the Gigabytes
  alias dT='du -hs * | awk '$1~"T"''  #show all files/folders with a size in the Terabytes

  # shortcuts for ls
  alias lh='ls -lh'          # sort in readable way
  alias la='ls -AlL'         # show hidden files and show size of files that are softlinked
  alias lx='ls -lXB'         # sort by extension
  alias lk='ls -lSr'         # sort by size, biggest last
  alias lc='ls -ltcr'        # sort by and show change time, most recent last
  alias lu='ls -ltur'        # sort by and show access time, most recent last
  alias lt='ls -ltr'         # sort by date, most recent last
  alias lm='ls -al |more'    # pipe through 'more'
  alias lr='ls -lR'          # recursive ls
  alias ld='ls -d */'        # list directories only
  alias ll='ls -l'
  alias lsr='tree -Csu'      # nice alternative to 'recursive ls'
  alias dirtree="ls -R | grep ":$" | sed -e 's/:$//' -e 's/[^-][^\/]*\//--/g' -e 's/^/ /' -e 's/-/|/'"

  #git shortcuts
  alias git-commit-count="git log --pretty=format:'' | wc -l"
  alias gc='git commit -m'
  alias gpom='git push origin main'
  alias gpomr='git push origin master'
  alias ga='git add'
  alias gpr='find . -type d -name .git -exec sh -c "cd \"{}\"/../ && pwd && git pull" \;'
  alias gclone='git clone git clone git@github.com:GITHUBID/$1'  # update your gitorganization or ID here
  alias gittree="git log --all --decorate --oneline --graph"  # commandline push history

  # HPC
  alias si="sinfo -o \"%20P %5D %14F %8z %10m %10d %11l %16f %N\""
  alias sq="squeue -o \"%8i %30j %4t %10u %20q %20a %10g %20P %10Q %5D %11l %11L %R %Z\""
  alias sacct='sacct --format JobID,Partition,Timelimit,Start,Elapsed,NodeList%20,ExitCode,ReqMem,MaxRSS,MaxVMSize,AllocCPUS'


###############################
## Never ending history:  never lose a command due to a history limit.
###############################

# Making never ending history!
  export HISTFILESIZE=
  export HISTSIZE=
  export HISTTIMEFORMAT="[%F %T] "
  export HISTFILE=~/.bash_eternal_history
  PROMPT_COMMAND="history -a; $PROMPT_COMMAND"
  # Avoid duplicates
  export HISTCONTROL=ignoredups:erasedups
  # When the shell exits, append to the history file instead of overwriting it
  shopt -s histappend
  # After each command, append to the history file and reread it and also add the pwd
  #export PROMPT_COMMAND='hpwd=$(history 1); hpwd="${hpwd# *[0-9]*  }"; if [[ ${hpwd%% *} == "cd" ]]; then cwd=$OLDPWD; else cwd=$PWD; fi; hpwd="${hpwd% ### *} ### $cwd"; history -s "$hpwd"; history -a; history -c; history -r'
  #export PROMPT_COMMAND="${PROMPT_COMMAND:+$PROMPT_COMMAND$'\n'}history -a; history -c; history -r"


###############################
## FUNCTIONS: Scripts can be added as functions in this file so you don't have to add it to your path.
###############################

# When you are in a hurry and want to add the current path to your PATH variable; not perminent
pathadd()
  { export PATH=$PATH:$1; }

# Handy Extract Program that will extract any file
function extract()
  {
       if [ -f $1 ] ; then
           case $1 in
               *.tar.bz2)   tar xvjf $1     ;;
               *.tar.gz)    tar xvzf $1     ;;
               *.bz2)       bunzip2 $1      ;;
               *.rar)       unrar x $1      ;;
               *.gz)        gunzip $1       ;;
               *.tar)       tar xvf $1      ;;
               *.tbz2)      tar xvjf $1     ;;
               *.tgz)       tar xvzf $1     ;;
               *.zip)       unzip $1        ;;
               *.Z)         uncompress $1   ;;
               *.7z)        7z x $1         ;;
               *.tar.xz)    tar xJvf $1     ;;
               *)           echo "'$1' cannot be extracted via >extract<" ;;
           esac
       else
           echo "'$1' is not a valid file"
       fi
  }

# Find a file with a pattern in name:
function ff() { find $(pwd -P) -type f -iname '*'$*'*' -ls ; }
function fd() { find $(pwd -P) -type d -iname '*'$*'*' -ls ; }

# It puts line number for grep matches, but only when it is at the end of the pipe
function grep()
  {
      if [[ -t 1 ]]; then
          command grep -n "$@"
      else
          command grep "$@"
      fi
  }

function body()
  {
  # print the header (the first line of input)
  # and then run the specified command on the body (the rest of the input)
  # use it in a pipeline, e.g. ps | body grep somepattern
      IFS= read -r header
      printf '%s\n' "$header"
      "$@"
  }