# Title: .bash_profile # Author: Frédéric CHEVALIER # Version: 3.2 # Created in: 2012-05-25 # Modified in: 2022-09-10 #==========# # Versions # #==========# # v3.2 - 2022-09-10: add timeout on welcome message # v3.1 - 2021-05-19: updates related to severs and SGE config changes (e.g., queue) / new env variable added # v3.0 - 2020-03-01: Linuxbrew added / Miniconda added / some Python env variables removed / R env variables removed / PATH setup improved / misc updates # v2.3 - 2019-03-10: alias updated / R hack for medusa2 added / no ssh key usage or storage for heron # v2.2 - 2017-04-23: server name updated / SSH connection through screen improved / welcome message improved # v2.1 - 2016-07-25: bug about space corrected / exit if not interactive (due to Grid Engine) # v2.0 - 2016-06-12: PATH setup improved / start_agent with multikey management / start_agent calling improved / screen behaviour added / welcome message improved / alias updated # v1.10 - 2015-08-17: Python lib adapted to the current version of Python / Consed env variable added / plocate updated to handle several db / pypm alias added / library path updated # v1.9 - 2015-04-20: Python env variable added / alias updated # v1.8 - 2014-12-02: proxy-display added (resolve $DISPLAY problem with screen) # v1.7 - 2014-10-22: alias added / conditional modification of PATH and LD_LIBRARY_PATH to be able to use eog and evince on other server (crow, ...) # v1.6 - 2014-10-15: alias added / LC* added / LS_COLORS removed / PATH updated / LD_LIBRARY_PATH updated # v1.5 - 2014-09-30: improve screen session detection to print welcome message at server connection even if screen session is running elsewhere # v1.4 - 2014-08-14: adapt behavior of the start screen regarding the screen program # v1.3 - 2014-08-06: part for SSH environment setup moved from .bashrc to avoid setting up SSH environment when connection to a node (qrsh) # v1.2 - 2014-07-09: behaviour modified when login to a node using qrsh (qrsh alias modified / if loop correction for message) # v1.1 - 2014-07-01: specific aliases needed for GridEngine added # v1.0 - 2014-06-28: rewriting for better interplay with .bashrc # v0.0 - 2012-05-25: creation #===============================# # Get the aliases and functions # #===============================# # If not running interactively, don't do anything ## Required because Grid Engine runs any shell as login shell by default leading to unwanted messages in the job status [[ -z "$PS1" ]] && return # Load bashrc file [[ -f ~/.bashrc ]] && source ~/.bashrc #==================# # Specific aliases # #==================# alias pqsub='qsub -V -cwd -o $HOME/status -j y -r y -S /bin/bash' alias pqsubR='qsub -V -cwd -o $HOME/status -j y -r y -S $(which Rscript)' alias pqrsh='qrsh -V -cwd -q interactive.q -pty y bash -li' alias plocate='locate -d "$mlocate_db"' alias xterm='xterm -bg black -fg white -rightbar -geometry 200x35' [[ $HOSTNAME =~ heron* ]] && alias ssh="ssh -o PreferredAuthentications=password -o PubkeyAuthentication=no" alias zeus='ssh zeus' alias mendel='ssh mendel' alias crow='ssh crow' alias bulmer='ssh bulmer' alias pypm="pypm -g" # Default parameter for pypm which is a package manager for python alias model_script_sh='cp $HOME/Templates/script.sh $1' #================================================# # User specific environment and startup programs # #================================================# #--------# # Locale # #--------# # Get with locale command export LANG=en_US.UTF-8 export LC_CTYPE=en_US.UTF-8 export LC_TIME=en_US.UTF-8 # Fix timestamp to english format (french connection problem) export LC_NUMERIC=en_US.UTF-8 # To always have . as decimal separator export LC_NAME=en_US.UTF-8 LC_ALL= bind 'set show-all-if-unmodified off' #-------# # Paths # #-------# # Package config export PKG_CONFIG_PATH=$(/usr/bin/pkg-config --variable pc_path pkg-config) # Path variable [[ $SHLVL -eq 1 ]] && export PATH=$HOME/local/bin:$HOME/local/share:$HOME/local/usr/local/bin:${PATH:+:$PATH} # Personal path # Linuxbrew [[ $SHLVL -eq 1 && -d "$HOME/.linuxbrew" ]] && eval $("$HOME/.linuxbrew/bin/brew" shellenv) # Use of personal /lib* if recent OS # Location of bamtools lib (source: http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/bamtools.htm) export LD_LIBRARY_PATH="${LD_LIBRARY_PATH:+$LD_LIBRARY_PATH:}$HOME/local/lib:$HOME/local/lib64" # Perl export PERL5LIB=~/local/lib/perl5/site_perl/5.18.2/x86_64-linux/auto:~/local/lib/perl5/5.18.2:~/local/lib/perl5/site_perl:~/local/lib/perl5/site_perl/5.18.2:~/local/lib/perl5/site_perl/5.18.2/x86_64-linux:~/local/lib/perl5/5.18.2/x86_64-linux:/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi:/usr/lib/perl5/site_perl/5.8.8:/usr/lib/perl5/site_perl:/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi:/usr/lib/perl5/vendor_perl/5.8.8:/usr/lib/perl5/vendor_perl:/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi:/usr/lib/perl5/5.8.8 # Python export PYTHONIOENCODING=utf-8 #----------# # Programs # #----------# # Locate export mlocate_db=$(ls -1 "$HOME/.mlocate.db"* | tr "\n" ":") # Consed export CONSED_HOME=~/local/bin/consed.d # Vim export VIMHOME=$HOME/.vim # Miniconda [[ -d "$HOME/.miniconda3" ]] && source "$HOME/.miniconda3/etc/profile.d/conda.sh" [[ -n $CONDA_DEFAULT_ENV ]] && conda activate $CONDA_DEFAULT_ENV # OPAM completion [[ $SHLVL -eq 1 ]] && source $HOME/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true # Git completion [[ -s "/etc/bash_completion.d/git" ]] && source /etc/bash_completion.d/git # Biom completion [[ $(which biom &> /dev/null ; echo $?) == 0 ]] && eval "$(_BIOM_COMPLETE=source biom)" # Linuxbrew completion [[ -s "$HOME/.linuxbrew/etc/bash_completion.d/brew" ]] && source "$HOME/.linuxbrew/etc/bash_completion.d/brew" # SSH environment setup SSH_KEY_LIST="$HOME/.ssh/key_list" # File with full path of keys (one per line) to load with start_agent [[ -f "$SSH_KEY_LIST" ]] && SSH_KEYS=($(cat $SSH_KEY_LIST)) #lifetime="-t 259200" # seconds => 3 days if [[ ! ($HOSTNAME =~ heron* || $HOSTNAME =~ compute.*) ]] then if [[ -n "$SSH_CONNECTION" ]] then # Source SSH settings, if applicable # Loading keys if [[ -f "${SSH_ENV}" ]] then source "$SSH_ENV" # Check if the ssh key is still stored if [[ $(ssh-add -l &> /dev/null; echo $?) != 0 ]] then pkill -u $USER ssh-agent eval start_agent $lifetime ${SSH_KEYS[@]} fi else eval start_agent $lifetime ${SSH_KEYS[@]} fi fi fi # Display forwarding # dependency: proxy-dsiplay if [[ ! ($HOSTNAME =~ heron* || $HOSTNAME =~ zeus* || $HOSTNAME =~ compute.*) && -n "$DISPLAY" && $(which proxy-display &> /dev/null; echo $?) == 0 ]] then proxy-display :99 fi # Improvement of screen usage (prevent screen session withing screen session) if [[ -n $STY || -n $LC_STY ]] then # Create a screen variable with level of screen if [[ -z $LC_STY ]] then export LC_STY=1 fi # ssh function to change the behaviour of ssh function ssh { /usr/bin/ssh -t $@ "export LC_STY=$(($LC_STY + 1)) && cd \"$PWD\" && exec $SHELL -l" } # Alias updated for i in $(alias | grep "screen" | cut -d " " -f 2 | cut -d "=" -f 1) do eval "alias $i=\"echo You are already in a screen session.\"" done [[ $LC_STY -gt 1 ]] && function screen { echo -e "This would start a within screen session. This is not recommanded. But if you need it, call $(which screen)." ; } fi #=================# # Welcome message # #=================# name=${HOSTNAME%%.*} nb=$(printf "%${#name}s\n" "" | sed "s/ /=/g") # Server message if [[ ! $HOSTNAME =~ compute.* && -z $STY && -z $LC_STY ]] then bash .welcome.msg fi # Info on disk space and cores if [[ ! ($HOSTNAME =~ heron* || $HOSTNAME =~ compute.*) && (-z $LC_STY || $LC_STY != 1) ]] then mydisk="/master" dspace=$(timeout 5s df -h 2> /dev/null) if [[ -n "$dspace" ]] then echo "" for i in $mydisk do [[ ! $(grep "$i " <<< "$dspace") ]] && continue echo -e "\033[33mSpace available on $i [% Used/Total/Free]:\033[00m $(grep "$i " <<< "$dspace" | awk '{print $5" / "$2" / "$4}' | head -n 1)" done echo "" fi if [[ ($name == "zeus") && (-z $LC_STY || $LC_STY != 1) ]] then cores=$(timeout 5s qstat -g c) echo -e "\033[33mCores available:\033[00m\n" echo -e "$cores\n" fi fi unset dspace