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

 # Title: .bash_profile

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

-# Version: 1.5

+# Version: 1.6

 # Created in: 2012-05-25

-# Modified in: 2014-09-30

+# Modified in: 2014-10-15

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

 # Versions #

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

+# 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

 # v1.3 - 2014-08-06: part for SSH environment setup moved from .bashrc to avoid setting up SSH environment when connection to a node (qrsh)

@@ -43,38 +44,37 @@ 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 model_script_sh='cp $HOME/Templates/script.sh $1'

-

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

 # User specific environment and startup programs #

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

-# Fix timestamp to english format (french connection problem)

-export LC_TIME=en_US.UTF-8

-

-# Specific locale variables (get with locale command)

-export LC_NUMERIC=en_US.UTF-8  # to always have . as decimal separator

-

-# Color definition

-export LS_COLORS='di=01;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:'

+# Locale variables (get with locale command)

+export LANG=en_US.UTF-8

+export LC_CTYPE=en_US.UTF-8

+export LC_TIME=en_US.UTF-8      # Fix timestamp to english format (french connection problem)

+export LC_NUMERIC=en_US.UTF-8   # To always have . as decimal separator

+export LC_NAME=en_US.UTF-8

+LC_ALL=

 # Path variable

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

-export PATH=$PATH:/opt/openmpi/bin:/usr/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/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 # 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 # 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" # :$HOME/local/lib64" #:$LD_LIBRARY_PATH"

+export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/local/lib:$HOME/local/lib64" #:$LD_LIBRARY_PATH"

 # Perl variables

-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

+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/

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

 # Vim

 export VIMHOME=$HOME/.vim