bashrcAndVimRC

.bashrc

PS1="\!@local:\W$ "
export CLICOLOR=true
export PATH=$PATH:/Users/dcaffrey/bin:/usr/local/mysql-5.1.41-osx10.5-x86/bin:/Users/dcaffrey/programs/muscle3.6_src:/Users/dcaffrey/programs/ViennaRNA-1.8.3/bin:/Users/dcaffrey/programs/blast-2.2.14/bin:/Users/dcaffrey/programs/hmmer-3.0-macosx-intel/binaries:/Users/dcaffrey/programs/wise2.2.0/src/bin:/Users/dcaffrey/programs/clustalw-2.0.12-macosx/:/Users/dcaffrey/programs/scwrl4:/Users/dcaffrey/programs/meme/bin:/usr/local/mysql/bin/:/Users/dcaffrey/programs/mrbayes/mrbayes-3.1.2:/Users/dcaffrey/programs/usr/local/bin:/Users/dcaffrey/programs/ligplot/hbplus:/Users/dcaffrey/programs/glam-src:/Users/dcaffrey/programs/rosetta3.1Bundles/rosetta_source/bin:/Users/adam/work/scripts/other:/Users/adam/work/scripts/ensembl/modules/:/Users/adam/bin:/Users/adam/work/scripts/other/modules
#PERL5LIB=${PERL5LIB}:/Users/dcaffrey/programs/bioPerl/bioperl-live:/Users/dcaffrey/programs/ensemblApi/ensembl/modules:/Users/dcaffrey/programs/ensemblApi/ensembl-compara/modules:/Users/dcaffrey/programs/ensemblApi/ensembl-variation/modules/:/Users/dcaffrey/programs/bioPerl/bioperl-live/Bio/DB/GFF/Adaptor/dbi:/Users/dcaffrey/programs/ensemblApi/ensembl-functgenomics/modules/
#export PERL5LIB

export HISTSIZE=10000
shopt -s histappend
export PROMPT_COMMAND='history -a'

export HISTTIMEFORMAT="%s "
PROMPT_COMMAND="${PROMPT_COMMAND:+$PROMPT_COMMAND ; }"'echo $$ $USER \
               "$(history 1)"  >> ~/.bash_eternal_history'
WISECONFIGDIR=/Users/dcaffrey/programs/wise2.2.0/wisecfg/
export WISECONFIGDIR
BLASTDB=/dbase1/blastdb
export BLASTDB
ROSETTA3_DB=/Users/dcaffrey/programs/rosetta3.1Bundles/rosetta_database
export ROSETTA3_DB
alias tarWork="tar -czf /Users/adam/workDirBackup.tar.gz  /Users/adam/work/"
alias openf="open -a finder ."
alias pf="cd /Users/adam/work/research/researchProjects/proteins/patchFinder"
alias tick="cd /Users/adam/work/research/researchProjects/immuneSystem/tickImmuneGenes"
alias lig="cd /Users/adam/work/research/researchProjects/proteins/patchFinder/datasets/ligAsite"
alias ligs="cd /Users/adam/work/research/researchProjects/proteins/patchFinder/scripts/ligAsite"
alias comp="cd /Users/adam/work/research/researchProjects/proteins/patchFinder/datasets/complexesFromUniprot"; 
export HISTCONTROL=erasedups
alias hpc1="ssh wespisea@hpcc01.umassmed.edu"
alias hpc3="ssh wespisea@hpcc03.umassmed.edu"
alias les="less"

export GNUTERM=aqua 
export DISPLAY=:0.0 

export BALL=" /Applications/BALLView.app/Contents/Frameworks"
export GSL_LIB_DIR=/Users/adam/bin/gsl-1.15
alias src="source ~/.bashrc"; 

alias darlingi="cd /Users/adam/work/research/researchProjects/immuneSystem/darlingi";

.vimrc

set number
syntax on
set term=ansi
set hlsearch

nnoremap j gj
nnoremap k gk

function! SuperTab()
    if (strpart(getline('.'),col('.')-2,1)=~'^\W\?$')
        return "\<Tab>"
    else
        return "\<C-n>"
    endif
endfunction
imap <Tab> <C-R>=SuperTab()<CR>