@@ -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

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

 # Title: .bash_profile

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

-# Version: 3.2

+# Version: 3.3

 # Created in: 2012-05-25

-# Modified in: 2022-09-10

+# Modified in: 2024-12-16

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

 # Versions #

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

+# 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

 # v3.0 - 2020-03-01: Linuxbrew added / Miniconda added / some Python env variables removed / R env variables removed / PATH setup improved / misc updates

@@ -120,8 +121,8 @@ export CONSED_HOME=~/local/bin/consed.d

 # Vim

 export VIMHOME=$HOME/.vim

-# Miniconda

-[[ -d "$HOME/.miniconda3" ]] && source "$HOME/.miniconda3/etc/profile.d/conda.sh"

+# Miniforge

+[[ -d "$HOME/.miniforge3" ]] && source "$HOME/.miniforge3/etc/profile.d/conda.sh"

 [[ -n $CONDA_DEFAULT_ENV ]]  && conda activate $CONDA_DEFAULT_ENV

 # OPAM completion

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

 # Title: .bash_profile

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

-# Version: 3.1

+# Version: 3.2

 # Created in: 2012-05-25

-# Modified in: 2021-05-19

+# 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

@@ -211,19 +212,24 @@ fi

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

 then

     mydisk="/master"

-    echo ""

-    for i in $mydisk

-    do

-        [[ ! $(df -h 2> /dev/null | grep "$i ") ]] && continue

-        echo -e "\033[33mSpace available on $i [% Used/Total/Free]:\033[00m $(df -h 2> /dev/null | grep "$i " | awk '{print $5" / "$2" / "$4}')"

-    done

-    echo ""

+    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"

-        qstat -g c

-        echo -e "\n"

+        echo -e "$cores\n"

     fi

 fi

+unset dspace

@@ -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

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

 # Title: .bash_profile

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

-# Version: 2.3

+# Version: 3.0

 # Created in: 2012-05-25

-# Modified in: 2019-03-10

+# Modified in: 2020-03-01

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

 # Versions #

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

+# 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)

@@ -37,10 +38,7 @@

 [[ -z "$PS1" ]] && return

 # Load bashrc file

-if [[ -f ~/.bashrc ]]

-then

-	source ~/.bashrc

-fi

+[[ -f ~/.bashrc ]] && source ~/.bashrc

@@ -89,14 +87,14 @@ bind 'set show-all-if-unmodified off'

 #-------#

 # Path variable

-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     # Personal path

+

+# Linuxbrew

+[[ $SHLVL -eq 1 && -d "$HOME/.linuxbrew" ]] && eval $("$HOME/.linuxbrew/bin/brew" shellenv)

 # Use of personal /lib* if recent OS

-if [[ $(lsb_release -r 2> /dev/null | cut -f 2) > 6.4 || $(grep -i "version_id" /etc/os-release 2> /dev/null | cut -d "\"" -f 2) > 6.4 ]]

-then

-    # 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"

-fi

+# 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.* ]]

@@ -114,10 +112,7 @@ fi

 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

 #----------#

@@ -133,20 +128,12 @@ 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}"

-

+# Miniconda

+[[ -d "$HOME/.miniconda3" ]] && source "$HOME/.miniconda3/etc/profile.d/conda.sh"

+[[ -n $CONDA_DEFAULT_ENV ]]  && conda activate $CONDA_DEFAULT_ENV

 # OPAM completion

-source $HOME/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true

+[[ $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

@@ -154,6 +141,9 @@ source $HOME/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true

 # 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

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

 # Title: .bash_profile

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

-# Version: 2.2

+# Version: 2.3

 # Created in: 2012-05-25

-# Modified in: 2017-04-23

+# Modified in: 2019-03-10

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

 # Versions #

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

+# 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

@@ -53,7 +54,8 @@ 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 medusa'

+[[ $HOSTNAME =~ heron* ]] && alias ssh="ssh -o PreferredAuthentications=password -o PubkeyAuthentication=no"

+alias medusa2='ssh medusa2'

 alias perseus='ssh perseus'

 alias mendel='ssh mendel'

 alias crow='ssh crow'

@@ -80,6 +82,7 @@ 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 #

@@ -102,6 +105,9 @@ then

     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

 # Perl

@@ -154,7 +160,7 @@ SSH_KEY_LIST="$HOME/.ssh/key_list"  # File with full path of keys (one per line)

 [[ -f "$SSH_KEY_LIST" ]] && SSH_KEYS=($(cat $SSH_KEY_LIST))

 #lifetime="-t 259200" # seconds => 3 days

-if [[ ! $HOSTNAME =~ compute.* ]]

+if [[ ! ($HOSTNAME =~ heron* || $HOSTNAME =~ compute.*) ]]

 then

     if [[ -n "$SSH_CONNECTION" ]]

     then

@@ -177,7 +183,7 @@ fi

 # Display forwarding

 # dependency: proxy-dsiplay

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

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

 then

     proxy-display :99

 fi

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

 # Title: .bash_profile

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

-# Version: 2.1

+# Version: 2.2

 # Created in: 2012-05-25

-# Modified in: 2016-07-25

+# Modified in: 2017-04-23

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

 # Versions #

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

+# 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

@@ -53,7 +54,7 @@ alias plocate='locate -d "$mlocate_db"'

 alias xterm='xterm -bg black -fg white -rightbar -geometry 200x35'

 alias medusa='ssh medusa'

-alias medusa2='ssh medusa2'

+alias perseus='ssh perseus'

 alias mendel='ssh mendel'

 alias crow='ssh crow'

 alias bulmer='ssh bulmer'

@@ -88,14 +89,14 @@ LC_ALL=

 export PATH=$HOME/local/bin:$HOME/local/share:$HOME/local/usr/local/bin:$PATH     # Personal path

 # Use of personal /lib* if recent OS

-if [[ $HOSTNAME != heron* && $(lsb_release -r | cut -f 2) > 6.4 ]]

+if [[ $(lsb_release -r 2> /dev/null | cut -f 2) > 6.4 || $(grep -i "version_id" /etc/os-release 2> /dev/null | cut -d "\"" -f 2) > 6.4 ]]

 then

     # 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"

 fi

-# Special paths for medusa and nodes

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

+# 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

@@ -137,6 +138,17 @@ fi

 export R_LIBS="${R_LIBS_HOME}/${R_version}"

+

+# OPAM completion

+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)"

+

+

 # 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))

@@ -165,37 +177,32 @@ fi

 # Display forwarding

 # dependency: proxy-dsiplay

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

+if [[ ! ($HOSTNAME =~ perseus* || $HOSTNAME =~ medusa* || $HOSTNAME =~ compute.*) && -n "$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 $STY || -f /tmp/${USER}_sty.lock ]]

+if [[ -n $STY || -n $LC_STY ]]

 then

-    # Create a screen lock with level of screen

-    if [[ -f /tmp/${USER}_sty.lock ]]

+    # Create a screen variable with level of screen

+    if [[ -z $LC_STY ]]

     then

-        export LC_STY=$(($(cat /tmp/${USER}_sty.lock) + 1))

-    else

         export LC_STY=1

     fi

     # ssh function to change the behaviour of ssh

     function ssh {

-        /usr/bin/ssh $@ "echo $LC_STY > /tmp/${USER}_sty.lock" &&

-        /usr/bin/ssh -t $@ "cd \"$PWD\" && exec $SHELL -l"

+        /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 running in a screen session.\""

+        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)." ; }

-

-    [[ -f /tmp/${USER}_sty.lock ]] && rm /tmp/${USER}_sty.lock

 fi

@@ -210,10 +217,7 @@ nb=$(printf "%${#name}s\n" "" | sed "s/ /=/g")

 # Server message

 if [[ ! $HOSTNAME =~ compute.* && -z $STY && -z $LC_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"

+    bash .welcome.msg

 fi

 # Info on disk space and cores

@@ -224,11 +228,11 @@ then

     for i in $mydisk

     do

         [[ ! $(df -h 2> /dev/null | grep "$i ") ]] && continue

-        echo -e "\033[33mSpace available on $i [%/Total/free]:\033[00m $(df -h 2> /dev/null | grep "$i " | awk '{print $5" / "$2" / "$4}')"

+        echo -e "\033[33mSpace available on $i [% Used/Total/Free]:\033[00m $(df -h 2> /dev/null | grep "$i " | awk '{print $5" / "$2" / "$4}')"

     done

     echo ""

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

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

     then

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

         qstat -g c

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

 # Title: .bash_profile

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

-# Version: 2.0

+# Version: 2.1

 # Created in: 2012-05-25

-# Modified in: 2016-06-12

+# Modified in: 2016-07-25

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

 # Versions #

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

+# 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

@@ -29,6 +30,11 @@

 # 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

 if [[ -f ~/.bashrc ]]

 then

 	source ~/.bashrc

@@ -134,7 +140,7 @@ export R_LIBS="${R_LIBS_HOME}/${R_version}"

 # 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=259200 # seconds => 3 days

+#lifetime="-t 259200" # seconds => 3 days

 if [[ ! $HOSTNAME =~ compute.* ]]

 then

@@ -149,10 +155,10 @@ then

             if [[ $(ssh-add -l &> /dev/null; echo $?) != 0 ]]

             then

                 pkill -u $USER ssh-agent

-                eval start_agent -t $lifetime ${SSH_KEYS[@]}

+                eval start_agent $lifetime ${SSH_KEYS[@]}

             fi

         else

-            eval start_agent -t $lifetime ${SSH_KEYS[@]}

+            eval start_agent $lifetime ${SSH_KEYS[@]}

         fi

     fi

 fi

@@ -211,7 +217,7 @@ then

 fi

 # Info on disk space and cores

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

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

 then

     mydisk="/master /data"

     echo ""

@@ -1,18 +1,19 @@

 # Title: .bash_profile

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

-# Version: 1.10

+# Version: 2.0

 # Created in: 2012-05-25

-# Modified in: 2015-08-17

+# Modified in: 2016-06-12

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

 # Versions #

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

+# 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, ...)

+# v1.7 - 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

@@ -45,11 +46,11 @@ 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 medusa='ssh medusa'

+alias medusa2='ssh medusa2'

+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'

@@ -78,9 +79,25 @@ LC_ALL=

 #-------#

 # Path variable

-export PATH=:$HOME/local/bin:$HOME/local/share:$HOME/local/usr/local/bin:$PATH     # Personal path

+export PATH=$HOME/local/bin:$HOME/local/share:$HOME/local/usr/local/bin:$PATH     # Personal path

-# Perl variables

+# Use of personal /lib* if recent OS

+if [[ $HOSTNAME != heron* && $(lsb_release -r | cut -f 2) > 6.4 ]]

+then

+    # 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"

+fi

+

+# Special paths for medusa and nodes

+if [[ $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

+fi

+

+# 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

@@ -89,18 +106,6 @@ 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 #

@@ -127,18 +132,27 @@ fi

 export R_LIBS="${R_LIBS_HOME}/${R_version}"

 # 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=259200 # seconds => 3 days

+

 if [[ ! $HOSTNAME =~ compute.* ]]

 then

     if [[ -n "$SSH_CONNECTION" ]]

     then

         # Source SSH settings, if applicable

+        # Loading keys

         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

+            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 -t $lifetime ${SSH_KEYS[@]}

+            fi

+        else

+            eval start_agent -t $lifetime ${SSH_KEYS[@]}

         fi

     fi

 fi

@@ -150,6 +164,34 @@ then

     proxy-display :99

 fi

+# Improvement of screen usage (prevent screen session withing screen session)

+if [[ -n $STY || -f /tmp/${USER}_sty.lock ]]

+then

+    # Create a screen lock with level of screen

+    if [[ -f /tmp/${USER}_sty.lock ]]

+    then

+        export LC_STY=$(($(cat /tmp/${USER}_sty.lock) + 1))

+    else

+        export LC_STY=1

+    fi

+

+    # ssh function to change the behaviour of ssh

+    function ssh {

+        /usr/bin/ssh $@ "echo $LC_STY > /tmp/${USER}_sty.lock" &&

+        /usr/bin/ssh -t $@ "cd \"$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 running 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)." ; }

+

+    [[ -f /tmp/${USER}_sty.lock ]] && rm /tmp/${USER}_sty.lock

+fi

+

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

@@ -159,17 +201,29 @@ fi

 name=${HOSTNAME%%.*}

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

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

+# Server message

+if [[ ! $HOSTNAME =~ compute.* && -z $STY && -z $LC_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"

-

+    echo -e "\n"

+fi

-    if [[ $(echo $name) == "medusa" || $(echo $name) == "medusa2" ]]

+# Info on disk space and cores

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

+then

+    mydisk="/master /data"

+    echo ""

+    for i in $mydisk

+    do

+        [[ ! $(df -h 2> /dev/null | grep "$i ") ]] && continue

+        echo -e "\033[33mSpace available on $i [%/Total/free]:\033[00m $(df -h 2> /dev/null | grep "$i " | awk '{print $5" / "$2" / "$4}')"

+    done

+    echo ""

+

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

     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"

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

 # Title: .bash_profile

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

-# Version: 1.9

+# Version: 1.10

 # Created in: 2012-05-25

-# Modified in: 2015-04-20

+# 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, ...)

@@ -41,7 +42,7 @@ fi

 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 "$HOME/.mlocate.db"'

+alias plocate='locate -d "$mlocate_db"'

 alias xterm='xterm -bg black -fg white -rightbar -geometry 200x35'

 alias medusa='ssh -Y medusa'

@@ -50,6 +51,7 @@ 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'

@@ -82,8 +84,10 @@ export PATH=:$HOME/local/bin:$HOME/local/share:$HOME/local/usr/local/bin:$PATH

 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 PYTHONPATH=$HOME/local/lib/python2.6/site-packages

+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.* ]]

@@ -94,7 +98,7 @@ then

     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"