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

 # Title: .bash_profile

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

-# Version: 3.0

+# Version: 3.1

 # Created in: 2012-05-25

-# Modified in: 2020-03-01

+# Modified in: 2021-05-19

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

 # Versions #

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

+# 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

@@ -48,13 +49,12 @@

 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 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 medusa2='ssh medusa2'

-alias perseus='ssh perseus'

+alias zeus='ssh zeus'

 alias mendel='ssh mendel'

 alias crow='ssh crow'

 alias bulmer='ssh bulmer'

@@ -86,27 +86,18 @@ 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     # Personal path

+[[ $SHLVL -eq 1 ]] && export PATH=$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="$LD_LIBRARY_PATH:$HOME/local/lib:$HOME/local/lib64"

-

-# Special paths for perseus, medusa and nodes

-if [[ $HOSTNAME =~ perseus* || $HOSTNAME =~ medusa* || $HOSTNAME =~ compute.* ]]

-then

-    # System 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

-    # Grid Engine path

-    export PATH=$PATH:/opt/gridengine/bin/linux-x64

-    # R

-    echo -e "\n\e[33mWarning:\e[00m Hard alias for R. If not needed, please edit .bash_profile.\n"

-    alias R="$HOME/local/pckg/R-3.3.1/bin/R"

-fi

+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

@@ -173,7 +164,7 @@ fi

 # Display forwarding

 # dependency: proxy-dsiplay

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

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

 then

     proxy-display :99

 fi

@@ -219,7 +210,7 @@ fi

 # Info on disk space and cores

 if [[ ! ($HOSTNAME =~ heron* || $HOSTNAME =~ compute.*) && (-z $LC_STY || $LC_STY != 1) ]]

 then

-    mydisk="/master /data"

+    mydisk="/master"

     echo ""

     for i in $mydisk

     do

@@ -228,7 +219,7 @@ then

     done

     echo ""

-    if [[ ($name == "perseus" || $name == "medusa2") && (-z $LC_STY || $LC_STY != 1) ]]

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

     then

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

         qstat -g c