@@ -1,14 +1,15 @@

 # Title: .bash_profile

 # Author: Frédéric CHEVALIER <f15.chevalier@gmail.com>

-# Version: 3.3

+# Version: 3.4

 # Created in: 2012-05-25

-# Modified in: 2024-12-16

+# Modified in: 2025-12-20

 #==========#

 # Versions #

 #==========#

+# v3.4 - 2025-12-20: switch SGE commands to Slurm commands / remove linuxbrew, system and perl lib paths, aliases

 # v3.3 - 2024-12-16: switch from miniconda to miniforge

 # 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

@@ -49,17 +50,13 @@

 # 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 psrun='srun --export=ALL --pty --partition=interactive 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 titan='ssh titan'

 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'

@@ -94,16 +91,6 @@ 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

@@ -134,16 +121,12 @@ export VIMHOME=$HOME/.vim

 # 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.*) ]]

+if [[ ! ($HOSTNAME =~ heron* || $HOSTNAME =~ n[0-9]*) ]]

 then

     if [[ -n "$SSH_CONNECTION" ]]

     then

@@ -166,7 +149,7 @@ fi

 # Display forwarding

 # dependency: proxy-dsiplay

-if [[ ! ($HOSTNAME =~ heron* || $HOSTNAME =~ zeus* || $HOSTNAME =~ compute.*) && -n "$DISPLAY" && $(which proxy-display &> /dev/null; echo $?) == 0 ]]

+if [[ ! ($HOSTNAME =~ heron* || $HOSTNAME =~ zeus* || $HOSTNAME =~ n[0-9]*) && -n "$DISPLAY" && $(which proxy-display &> /dev/null; echo $?) == 0 ]]

 then

     proxy-display :99

 fi

@@ -204,13 +187,13 @@ name=${HOSTNAME%%.*}

 nb=$(printf "%${#name}s\n" "" | sed "s/ /=/g")

 # Server message

-if [[ ! $HOSTNAME =~ compute.* && -z $STY && -z $LC_STY ]]

+if [[ ! $HOSTNAME =~ n[0-9]* && -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) ]]

+if [[ ! ($HOSTNAME =~ heron* || $HOSTNAME =~ n[0-9].*) && (-z $LC_STY || $LC_STY != 1) ]]

 then

     mydisk="/master"

     dspace=$(timeout 5s df -h 2> /dev/null)

@@ -227,7 +210,7 @@ then

     if [[ ($name == "zeus") && (-z $LC_STY || $LC_STY != 1) ]]

     then

-        cores=$(timeout 5s qstat -g c)

+        cores=$(timeout 5s sinfo -o "%P|%a|%l|%D|%t|%C" | column -t -s "|")

         echo -e "\033[33mCores available:\033[00m\n"

         echo -e "$cores\n"

     fi