@@ -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

@@ -1,23 +1,37 @@

-  P. ::.::::i:i:i:i:i:::LF  .O@v  

-  iBriLZXFqG0ZNEEGZOZGNPr  7B@i   

-   :@BG57               i0@BL     

-     7B@Mkr;vkEZ2r. .LO@BN:       

-       ,XB@XLvJ,.:5M@M5:          

-          :PMM0SL77v              

-        .:Lk0jivq0PY7i:.          

-     .7O@@BFi. .:vq@B@BMkLi.      

-   ,rO@PX5uukP0qX2Uu11SFOBMF2r         ===================*=========

-  ujBO                   .uMN8@i 

-  @G@G5B@B@B@B@B@@@B@B@@@G0B@8OB.              Welcome on HOSTNAME

-  8@qMX,                    .EN@L 

-   Y@Mk7. ,:i:iirirrr;rirr:  2@B       ===================*=========

-     LM@MXJ2q@OGZOMBMMOMNr:7O@E   

-       .UM@ZUr:         .Y@Bq,    

-           rkMO82v:, ,LGMS:       

-               ikG8ESv;r:         

-             .:72EP7L0q1YJ7i.     

-          iuOM@B@Ek2SqMB@MME1JL   

-       :L0Eu,              iFS2@7 

-    .rG@@M5vYUSkPSXkXkXSX1JruMPU@.

-  :iFBY7rrrLvLvYLLLLvYvYLLLLiLUJ@:

- r1FB                        .7PP 

+#!/bin/bash

+

+name="${HOSTNAME%%.*}"

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

+nb=$(echo $name | sed "s/./=/g")

+

+myuptime=$(uptime | sed "s/  */ /g ; s/,/\\n/g" | sed -n "1p" | sed "s/.*up //g" |sed -r "s/([0-9]*)/\\\e[1;92m\1\\\e[0m/g")

+myusers=$(uptime | sed "s/  */ /g ; s/,/\\n/g" | sed "s/^ *//g" | sed -n "2p" | sed -r "s/([0-9]*)/\\\e[1;92m\1\\\e[0m/g")

+myOS=$(lsb_release -d 2> /dev/null | sed "s/  */\\t/g" | cut -f 2-| sed "s/\\t/ /g")

+[[ -z "$myOS" ]] && myOS=$(grep "PRETTY_NAME=" /etc/os-release 2> /dev/null | cut -d "\"" -f 2)

+

+

+echo -e "

+  P. ::.::::i:i:i:i:i:::LF  .O@v  

+  iBriLZXFqG0ZNEEGZOZGNPr  7B@i   

+   :@BG57               i0@BL     

+     7B@Mkr;vkEZ2r. .LO@BN:       

+       ,XB@XLvJ,.:5M@M5:          

+          :PMM0SL77v              

+        .:Lk0jivq0PY7idd:.        

+     .7O@@BFi. .:vq@B@BMkjp.     

+   ,rOO                   MF2r         ===================${nb}=========

+  ujBO@PX5uukP0qX2Uu11SFO.uMN8@i 

+  @G@G5B@B@B@B@B@@@B@B@@@G0B@8OB.              Welcome on \e[1;35m$name\e[0m

+  8@qMX,                    .EN@L 

+   Y@Mk7. ,:i:iirirrr;rirr:  2@B       ===================${nb}=========

+     LM@MXJ2q@OGZOMBMMOMNr:7O@E   

+       .UM@ZUr:         .Y@Bq,    

+           rkMO82v:, ,LGMS:                 \e[36mUptime\e[0m: $myuptime 

+               ikG8ESv;r:                    \e[36mUsers\e[0m: $myusers

+             .:72EP7L0q1YJ7i.                   \e[36mOS\e[0m: $myOS 

+          iuOM@B@Ek2SqMB@MME1JL   

+       :L0Eu,              iFS2@7 

+    .rG@@M5vYUSkPSXkXkXSX1JruMPU@.

+  :iFBY7rrrLvLvYLLLLvYvYLLLLiLUJ@:

+ r1FB                        .7PP

+"