# ~/.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 anythingcase $- in *i*) ;; *) return;;esac# don't put duplicate lines or lines starting with space in the history.# See bash(1) for more optionsHISTCONTROL=ignoreboth# append to the history file, don't overwrite itshopt -s histappend# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)HISTSIZE=1000HISTFILESIZE=2000# check the window size after each command and, if necessary,# update the values of LINES and COLUMNS.shopt -s checkwinsize# If set, the pattern "**" used in a pathname expansion context will# match all files and zero or more directories and subdirectories.#shopt -s globstar# make less more friendly for non-text input files, see lesspipe(1)[ -x /usr/bin/lesspipe ] && eval "$(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 "$TERM" in xterm-color|*-256color) color_prompt=yes;;esac# uncomment for a colored prompt, if the terminal has the capability; turned# off by default to not distract the user: the focus in a terminal window# should be on the output of commands, not on the prompt#force_color_prompt=yesif [ -n "$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= fifiif [ "$color_prompt" = yes ]; then PS1='${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\$ 'fiunset color_prompt force_color_prompt# If this is an xterm set the title to user@host:dircase "$TERM" inxterm*|rxvt*) PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1" ;;*) ;;esac# enable color support of ls and also add handy aliasesif [ -x /usr/bin/dircolors ]; then test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)" alias ls='ls --color=auto' #alias dir='dir --color=auto' #alias vdir='vdir --color=auto' alias grep='grep --color=auto' alias fgrep='fgrep --color=auto' alias egrep='egrep --color=auto'fi# colored GCC warnings and errors#export GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'# some more ls aliasesalias ll='ls -alF'alias la='ls -A'alias l='ls -CF'alias h='history'alias myip="ifconfig enp3s0f1 | grep 'inet'| sed -e '2d' -e 's/^.*inet/ /g' | cut -d ' ' -f 3"MYIP=$(myip)# Add an "alert" alias for long running commands. Use like so:# sleep 10; alertalias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal || echo error)" "$(history|tail -n1|sed -e '\''s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\'')"'# Alias definitions.# You may want to put all your additions into a separate file like# ~/.bash_aliases, instead of adding them here directly.# See /usr/share/doc/bash-doc/examples in the bash-doc package.if [ -f ~/.bash_aliases ]; then . ~/.bash_aliasesfi# enable programmable completion features (you don't need to enable# this, if it's already enabled in /etc/bash.bashrc and /etc/profile# sources /etc/bash.bashrc).if ! shopt -oq posix; then if [ -f /usr/share/bash-completion/bash_completion ]; then . /usr/share/bash-completion/bash_completion elif [ -f /etc/bash_completion ]; then . /etc/bash_completion fifiPATH=$PATH:~/d/software/biosoft/sratoolkit/sratoolkit.2.9.6-1-ubuntu64/bin# >>> conda initialize >>># !! Contents within this block are managed by 'conda init' !!__conda_setup="$('/home/rock/d/software/biosoft/anaconda/[/home/rock/d/software/biosoft/anaconda]/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"if [ $? -eq 0 ]; then eval "$__conda_setup"else if [ -f "/home/rock/d/software/biosoft/anaconda/[/home/rock/d/software/biosoft/anaconda]/etc/profile.d/conda.sh" ]; then . "/home/rock/d/software/biosoft/anaconda/[/home/rock/d/software/biosoft/anaconda]/etc/profile.d/conda.sh" else export PATH="/home/rock/d/software/biosoft/anaconda/[/home/rock/d/software/biosoft/anaconda]/bin:$PATH" fifiunset __conda_setup# <<< conda initialize <<<PATH=$PATH:~/d/software/biosoft/anaconda/anaconda/binPATH=$PATH:~/d/software/biosoft/HISAT/hisat-0.1.6-betaPATH=$PATH:~/d/software/biosoft/fastqc/FastQCPATH=$PATH:~/d/software/biosoft/samtools/bin