@@ -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"