My linux environment

bashrc_goodies.sh

# ~/.bashrc: executed by bash(1) for non-login shells.
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples

# If not running interactively, don't do anything
case $- in
    *i*) ;;
      *) return;;
esac

# don't put duplicate lines or lines starting with space in the history.
# See bash(1) for more options
HISTCONTROL=ignoreboth

# append to the history file, don't overwrite it
shopt -s histappend

# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
HISTSIZE=1000
HISTFILESIZE=2000

# check the window size after each command and, if necessary,
# update the values of LINES and COLUMNS.
shopt -s checkwinsize

# If set, the pattern "**" used in a pathname expansion context will
# match all files and zero or more directories and subdirectories.
#shopt -s globstar

# make less more friendly for non-text input files, see lesspipe(1)
#[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"

# set variable identifying the chroot you work in (used in the prompt below)
if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
    debian_chroot=$(cat /etc/debian_chroot)
fi

# set a fancy prompt (non-color, unless we know we "want" color)
case "$TERM" in
    xterm-color) color_prompt=yes;;
esac

# uncomment for a colored prompt, if the terminal has the capability; turned
# off by default to not distract the user: the focus in a terminal window
# should be on the output of commands, not on the prompt
force_color_prompt=yes

if [ -n "$force_color_prompt" ]; then
    if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
	# We have color support; assume it's compliant with Ecma-48
	# (ISO/IEC-6429). (Lack of such support is extremely rare, and such
	# a case would tend to support setf rather than setaf.)
	color_prompt=yes
    else
	color_prompt=
    fi
fi


# set the colors for terminal: https://help.ubuntu.com/community/CustomizingBashPrompt
# ANSI color codes
RS="\[\033[0m\]"    # reset
HC="\[\033[1m\]"    # hicolor
UL="\[\033[4m\]"    # underline
INV="\[\033[7m\]"   # inverse background and foreground
FBLK="\[\033[30m\]" # foreground black
FRED="\[\033[31m\]" # foreground red
FGRN="\[\033[32m\]" # foreground green
FYEL="\[\033[33m\]" # foreground yellow
FBLE="\[\033[34m\]" # foreground blue
FMAG="\[\033[35m\]" # foreground magenta
FCYN="\[\033[36m\]" # foreground cyan
FWHT="\[\033[37m\]" # foreground white
BBLK="\[\033[40m\]" # background black
BRED="\[\033[41m\]" # background red
BGRN="\[\033[42m\]" # background green
BYEL="\[\033[43m\]" # background yellow
BBLE="\[\033[44m\]" # background blue
BMAG="\[\033[45m\]" # background magenta
BCYN="\[\033[46m\]" # background cyan
BWHT="\[\033[47m\]" # background white


if [ "$color_prompt" = yes ]; then
    PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\W\[\033[00m\]\$ '
else
    PS1='${debian_chroot:+($debian_chroot)}\u@\h:\W\$ '
fi
unset color_prompt force_color_prompt


# If this is an xterm set the title to user@host:dir
case "$TERM" in
xterm*|rxvt*)
    PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
    ;;
*)
    ;;
esac

# enable color support of ls and also add handy aliases
if [ -x /usr/bin/dircolors ]; then
    test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
    alias ls='ls --color=auto'
    #alias dir='dir --color=auto'
    #alias vdir='vdir --color=auto'

    #alias grep='grep --color=auto'
    #alias fgrep='fgrep --color=auto'
    #alias egrep='egrep --color=auto'
fi

# some more ls aliases
alias ll='ls -alFh'
alias la='ls -A'
alias l='ls -CF'

alias igv='~/bin/IGV_2.3.40/igv.sh'

alias ketting='cd /fsimb/groups/imb-kettinggr/'
alias genome='cd ~/imb-kettinggr/genomes/'
alias scratch='cd /local/scratch1/imb-kettinggr/adomingues/'

function ptar() {
   tar cf - "$1" | pigz -9 -p 2 > "$1".tar.gz
}


# This is GOLD for finding out what is taking so much space on your drives!
alias diskspace="du -S | sort -n -r |more"
# extracts any type of file:
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        ;;
           *)           echo "don't know how to extract '$1'..." ;;
       esac
   else
       echo "'$1' is not a valid file!"
   fi
 }

# No more cd ../../../.. but up 4 - move up across directories
up(){
  local d=""
  limit=$1
  for ((i=1 ; i <= limit ; i++))
    do
      d=$d/..
    done
  d=$(echo $d | sed 's/^\///')
  if [ -z "$d" ]; then
    d=..
  fi
  cd $d
}


# Alias definitions.
# You may want to put all your additions into a separate file like
# ~/.bash_aliases, instead of adding them here directly.
# See /usr/share/doc/bash-doc/examples in the bash-doc package.

if [ -f ~/.bash_aliases ]; then
    . ~/.bash_aliases
fi

# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if ! shopt -oq posix; then
  if [ -f /usr/share/bash-completion/bash_completion ]; then
    . /usr/share/bash-completion/bash_completion
  elif [ -f /etc/bash_completion ]; then
    . /etc/bash_completion
  fi
fi


# inspect the first and last 2 lines of a file
i() { 
   (head -n 2; tail -n 2) < $1 | column -t 
}


# my paths
PATH="$PATH:~/bin/bedtools-2.17.0/bin/"
PATH="$PATH:~/.local/bin/"

# overwrite locales settings from personal laptop:
export LANG=en_US.UTF-8
export LANGUAGE=en_US:en
export LC_CTYPE="en_US.UTF-8"
export LC_NUMERIC="en_US.UTF-8"
export LC_TIME="en_US.UTF-8"
export LC_COLLATE="en_US.UTF-8"
export LC_MONETARY="en_US.UTF-8"
export LC_MESSAGES="en_US.UTF-8"
export LC_PAPER="en_US.UTF-8"
export LC_NAME="en_US.UTF-8"
export LC_ADDRESS="en_US.UTF-8"
export LC_TELEPHONE="en_US.UTF-8"
export LC_MEASUREMENT="en_US.UTF-8"
export LC_IDENTIFICATION="en_US.UTF-8"
export LC_ALL=

export PATH=/home/adomingu/bin:/cluster/software/lsf/9.1/linux2.6-glibc2.3-x86_64/etc:/cluster/software/lsf/9.1/linux2.6-glibc2.3-x86_64/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:~/bin/bedtools-2.17.0/bin/:~/.local/bin/:/home/adomingu/bin/sratoolkit.2.3.5-2-ubuntu64/bin
export PATH=/home/adomingu/bin:/cluster/software/lsf/9.1/linux2.6-glibc2.3-x86_64/etc:/cluster/software/lsf/9.1/linux2.6-glibc2.3-x86_64/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:/home/adomingu/bin/bedtools-2.17.0/bin/:/home/adomingu/.local/bin/:/home/adomingu/bin/sratoolkit.2.3.5-2-ubuntu64/bin:/home/adomingu/bin/sratoolkit.2.4.4-ubuntu64/bin
export PATH=/home/adomingu/bin:/home/adomingu/bin:/cluster/software/lsf/9.1/linux2.6-glibc2.3-x86_64/etc:/cluster/software/lsf/9.1/linux2.6-glibc2.3-x86_64/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:/home/adomingu/bin/bedtools-2.17.0/bin/:/home/adomingu/.local/bin/:/home/adomingu/bin/sratoolkit.2.3.5-2-ubuntu64/bin:/home/adomingu/bin/sratoolkit.2.4.4-ubuntu64/bin:/home/adomingu/.aspera/connect/bin/:/home/adomingu/edirect:/home/adomingu/bin/bedtools2/bin/
export JAVA_HOME=/usr/lib/jvm/java-6-openjdk-amd64/jre
export PATH=/usr/lib/jvm/java-6-openjdk-amd64/jre/bin:$PATH
export PATH=~/bin/ngsutils/bin:$PATH
export PATH=~/bin/ncbi-blast-2.2.31+/bin:$PATH
export PATH=~/bin/pingpongpro-v1.0-linux64:$PATH
export PATH=/fsimb/groups/imb-kettinggr/common_bin/R/R-3.3.2/bin/:$PATH
export PATH=/fsimb/groups/imb-kettinggr/common_bin/R/3.3.2_LIBS:$PATH

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/fsimb/groups/imb-kettinggr/common_bin/R/R-3.3.2/bin
export R_HOME=/home/adomingu/imb-kettinggr/common_bin/R/R-3.3.2/lib64/R

PATH=$PATH:"/local/scratch1/imb-kettinggr/adomingues/projects/GSM1505439/scripts/renetseqanalysisandreadduplication"
export PATH

PATH=$PATH:"/local/scratch1/imb-kettinggr/adomingues/GSM1505439/results/sterling"
export PATH


# all new files will be available to every one in the group
umask 0007