# Title: .bash_profile # Author: Frédéric CHEVALIER # Version: 1.10 # Created in: 2012-05-25 # Modified in: 2015-08-17 #==========# # Versions # #==========# # 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 [[ -f ~/.bashrc ]] then source ~/.bashrc fi #==================# # 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 $(which Rscript)' alias pqrsh='qrsh -V -cwd -pty y bash -li' alias plocate='locate -d "$mlocate_db"' alias xterm='xterm -bg black -fg white -rightbar -geometry 200x35' alias medusa='ssh -Y medusa' alias medusa2='ssh -Y medusa2' alias mendel='ssh -Y mendel' alias crow='ssh -Y crow' alias bulmer='ssh -Y 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 $1' #================================================# # User specific environment and startup programs # #================================================# #--------# # Locale # #--------# # Get with locale command export LANG=en_US.UTF-8 export LC_CTYPE=en_US.UTF-8 export LC_TIME=en_US.UTF-8 # Fix timestamp to english format (french connection problem) export LC_NUMERIC=en_US.UTF-8 # To always have . as decimal separator export LC_NAME=en_US.UTF-8 LC_ALL= #-------# # Paths # #-------# # Path variable export PATH=:$HOME/local/bin:$HOME/local/share:$HOME/local/usr/local/bin:$PATH # Personal path # Perl variables export PERL5LIB=~/local/lib/perl5/site_perl/5.18.2/x86_64-linux/auto:~/local/lib/perl5/5.18.2:~/local/lib/perl5/site_perl:~/local/lib/perl5/site_perl/5.18.2:~/local/lib/perl5/site_perl/5.18.2/x86_64-linux:~/local/lib/perl5/5.18.2/x86_64-linux:/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi:/usr/lib/perl5/site_perl/5.8.8:/usr/lib/perl5/site_perl:/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi:/usr/lib/perl5/vendor_perl/5.8.8:/usr/lib/perl5/vendor_perl:/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi:/usr/lib/perl5/5.8.8 # Python python_version=$(python --version 2>&1 | cut -d " " -f2 | cut -d "." -f -2) export PYTHONPATH=$HOME/local/lib/python${python_version}/site-packages export PYTHONIOENCODING=utf-8 unset python_version # Special paths for medusa and nodes if [[ $HOSTNAME =~ medusa* || $HOSTNAME =~ compute.* ]] then # Path variable export PATH=$HOME/local/bin:$HOME/local/share:$HOME/local/usr/local/bin # Personal path export PATH=$PATH:/opt/openmpi/bin:/opt/bio/ncbi/bin:/opt/bio/mpiblast/bin:/opt/bio/hmmer/bin:/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:/opt/bio/tcoffee/bin:/opt/bio/phylip/exe:/opt/bio/mrbayes:/opt/bio/fasta:/opt/bio/glimmer/bin:/opt/bio/glimmer/scripts:/opt/bio/gromacs/bin:/opt/bio/gmap/bin:/opt/bio/tigr/bin:/opt/bio/autodocksuite/bin:/opt/bio/wgs/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/rocks/bin:/opt/rocks/sbin:/opt/condor/bin:/opt/condor/sbin:/opt/gridengine/bin/lx26-amd64:/usr/bin:/usr/local/bin:/bin:/usr/java/latest/bin # System path export PATH=$PATH:/opt/gridengine/bin/linux-x64 # System path needed for the new medusa # Location of bamtools lib (source: http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/bamtools.htm) export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/local/lib:$HOME/local/lib64" # Otherwise pb with heron #:$LD_LIBRARY_PATH" fi #----------# # Programs # #----------# # Locate export mlocate_db=$(ls -1 "$HOME/.mlocate.db"* | tr "\n" ":") # Consed export CONSED_HOME=~/local/bin/consed.d # Vim export VIMHOME=$HOME/.vim # R R_version=$(R --version | head -1 | cut -d " " -f 3) export R_LIBS_HOME="$HOME/.R-libs" if [[ ! -d "${R_LIBS_HOME}/${R_version}" ]] then mkdir "${R_LIBS_HOME}/${R_version}" fi export R_LIBS="${R_LIBS_HOME}/${R_version}" # SSH environment setup if [[ ! $HOSTNAME =~ compute.* ]] then if [[ -n "$SSH_CONNECTION" ]] then # Source SSH settings, if applicable if [[ -f "${SSH_ENV}" ]] then source "${SSH_ENV}" > /dev/null #ps ${SSH_AGENT_PID} doesn't work under cywgin ps -ef | grep ${SSH_AGENT_PID} | grep ssh-agent$ > /dev/null || start_agent else start_agent fi fi fi # Display forwarding # dependency: proxy-dsiplay if [[ ! ($HOSTNAME =~ medusa* || $HOSTNAME =~ compute.*) && -n "$DISPLAY" && $(which proxy-display &> /dev/null; echo $?) == 0 ]] then proxy-display :99 fi #=================# # Welcome message # #=================# name=${HOSTNAME%%.*} nb=$(printf "%${#name}s\n" "" | sed "s/ /=/g") if [[ ! $HOSTNAME =~ compute.* && -z $STY ]] then nb=$nb======= echo -e "\n\n" cat .welcome.msg | sed "s/HOSTNAME/$(echo $name Server | sed "s/^[m,h]/\U&/")/" | sed "s/=\*/$nb/g" echo -e "\n\n" if [[ $(echo $name) == "medusa" || $(echo $name) == "medusa2" ]] then echo -e "\033[33mSpace available on /master [%/Total/free]:\033[00m $(df -h | grep "/master " | awk '{print $5" / "$2" / "$4}')\n" echo -e "\033[33mCores available:\033[00m\n" qstat -g c echo -e "\n" fi fi