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# .bash_profile
# Get the aliases and functions
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi
#Customized home at /data
MYHOME=/data/users/zl222
# User specific environment and startup programs
if [ -f $HOME/shortcuts ]; then
source $HOME/shortcuts
fi
for i in `ls -d $MYHOME/bin/* $MYHOME/svn/* $MYHOME/svn/John_scripts/* /data/apps/* /data/bin/* `; do
if [ -d $i ] ; then
PATH=$PATH:$i
fi
done
PATH=$PATH:$MYHOME/bin:$MYHOME/bin/blast/bin
PATH=/data/apps/samtools-0.1.17:$PATH
alias qstat="qstat -u '*'"
alias screen="/usr/bin/screen -D -R"
alias rm="$MYHOME/bin/del.sh"
alias undel="$MYHOME/bin/del.sh -u"
alias ls="ls --color"
alias ld="ls -d"
alias c="clear"
alias l="ls -alh"
alias lf="ls -F|grep /"
alias lt="ls -tlr"
alias mv="mv -i"
alias cp="cp -pi"
alias diff="diff -b"
PERL5LIB=$MYHOME/perllib:$MYHOME/perllib/lib64/perl5/site_perl/5.8.5:$MYHOME/perlib/lib/perl5/site_perl/5.8.5
PERL5LIB=$PERL5LIB:$MYHOME/perllib/lib64/perl5/site_perl/5.8.8:$MYHOME/perlib/lib/perl5/site_perl/5.8.8:$MYHOME/perllib/lib/perl5/site_perl/5.8.8
PERL5LIB=${PERL5LIB}:$MYHOME/cvs/ensembl/modules
PERL5LIB=${PERL5LIB}:$MYHOME/cvs/ensembl-compara/modules
PERL5LIB=${PERL5LIB}:$MYHOME/cvs/ensembl-functgenomics/modules
PERL5LIB=${PERL5LIB}:$MYHOME/svn/John_scripts/modules
PERL5LIB=${PERL5LIB}:$MYHOME/bin/ViennaRNA/Perl
export PERL5LIB
export R_LIBS_USER=~/R:/data/apps/R_library
export BOWTIE_INDEXES=$MYHOME/Projects/genomes/bowtie_indexes
export PATH
unset USERNAME
cd $MYHOME
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