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.bashrc

# .bash_profile

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

# User specific aliases and functions

#PATH=/home/obotvinnik/bin/jre1.7.0_07/bin:/home/obotvinnik/packages/java-genomics-toolkit:/home/obotvinnik/packages/epd-7.3-2-rh3-x86_64/bin:$HOME/bin:$PATH:$HOME/packages/weblogo

#PATH=$PATH:/home/obotvinnik/packages/homer/.//bin/

#export PATH

alias 'ucsd-git-pull'='env GIT_SSL_NO_VERIFY=true git pull origin master'
alias 'ucsd-git-push'='env GIT_SSL_NO_VERIFY=true git push origin master'

#export PATH

eval "`dircolors -b ~/.dircolors_test`"
alias ls='ls --color=auto'
alias ll='ls -lh'
alias la='ls -lha' 
alias l='ls -CF' # .bashrc

# Ipython alias with static port. `&` indicates that the process should run in the background
alias ipy='ipython notebook --port 8988 &'

# install python modules cleanly
alias pycleanbuildinstall='python setup.py clean ; python setup.py build ; python setup.py install'

alias rotation='cd ~/rotations/q3-spring-pevzner'
alias qstato='qstat -u obotvinnik'
alias showqo='showq -u obotvinnik'
alias conf='./configure --prefix /home/obotvinnik ; make ; make install'

export [email protected]




alias vi='emacs' # LOL :)
alias vim='emacs'

# Add my personal pythonpath for python packages
#export PYTHONPATH=$PYTHONPATH
export EDITOR=/usr/bin/emacs

# make sure we have the right samtools
#export PATH=/home/yeo-lab/software/bin/samtools:$PATH
#export PATH=$PATH:/home/yeo-lab/software/apache-maven-3.1.0/bin
#export CLASSPATH=/home/yeo-lab/software/colt/lib/colt.jar:/home/yeo-lab/software/colt/lib/concurrent.jar:$CLASSPATH 

# Activate my virtual environment
#source ~/obot_virtualenv/bin/activate

# Force usage of the virtual environment packages
#export PYTHONPATH=~/obot_virtualenv/lib/python2.7/site-packages/:$PYTHONPATH


alias chmodpy='chgrp -R yeo-group /home/yeo-lab/software/lib/python2.7/site-packages ; chmod -R 775 /home/yeo-lab/software/lib/python2.7/site-packages'


#source ~/virtualenvs/envy/bin/activate
#export PATH=~/virtualenvs/envy/bin:$HOME/bin:/projects/ps-yeolab/software/bin:$PATH

# make sure all virtualenv packages get imported and we never use anything from /opt, and use yeolab stuff as a last resort.
#export PYTHONPATH=$(python -c 'import os; print ":".join(set(p for p in os.environ["PYTHONPATH"].split(":") if p and ("opt" not in p and "yeo" not in p)))')
#export PYTHONPATH=$PYTHONPATH:/projects/ps-yeolab/software/lib/python2.7/site-packages

#OLD_LD_LIBRARY_PATH=$LD_LIBRARY_PATH
#export LD_LIBRARY_PATH=
#source /opt/intel/composer_xe_2013.1.117/bin/compilervars.sh intel64
#source /opt/intel/composer_xe_2013.1.117/mkl/bin/mklvars.sh intel64
#export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$OLD_LD_LIBRARY_PATH




export IPYNB_PORT=8812
export IPYNB_MINUTES=12
alias sshcluster="ssh [email protected] -L $IPYNB_PORT:localhost:$IPYNB_PORT"
# added by Anaconda 1.9.1 installer
#export PATH="/projects/ps-yeolab/software/anaconda/bin:~/bin:$PATH"
#export PYTHONPATH=

alias ipynb="IPYTHONDIR=/tmp/ipython jupyter notebook --no-browser --port 7700 &"
alias sshtscc="ssh -NR 7700:localhost:7700 tscc-login2 &"

if [ -f ~/.git-completion.bash ]; then
  . ~/.git-completion.bash
fi
# added by Anaconda 2.1.0 installer
#export PATH="/home/obotvinnik/anaconda/bin:$PATH"

export PERL_MM_USE_DEFAULT=1
source ~/gscripts/bashrc/tscc_bash_settings_current
#source activate olga

# added by Anaconda 2.2.0 installer
export PATH="~/bin:$PATH"
export PATH="/home/obotvinnik/anaconda/bin:$PATH"
alias dropbox="python $(which dropbox.py)"

# Add variables of paths with and without yeo-based paths and ld library paths
export LD_LIBRARY_PATH_NO_YEO="/opt/python/lib:/opt/gnu/gcc/lib64:/opt/gnu/gmp/lib:/opt/gnu/mpfr/lib:/opt/gnu/mpc/lib:/opt/openmpi/gnu/ib/lib:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/intel64/gcc4.4:/opt/sdsc/lib:/opt/biotools/bamtools/lib/bamtools:/opt/boost/gnu/lib:/opt/biotools/fastx/lib:/opt/biotools/squid/lib:/opt/biotools/ViennaRNA/lib"

export PATH_NO_YEO="/home/obotvinnik/anaconda/bin:/home/obotvinnik/bin:/home/obotvinnik/bin:/opt/openmpi/gnu/ib/bin:/home/obotvinnik/anaconda/bin:/home/obotvinnik/bin:/home/obotvinnik/bin:/opt/python/bin:/opt/gnu/gcc/bin:/opt/openmpi/intel/ib/bin:/opt/intel/composer_xe_2013_sp1.2.144/bin/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/bin/intel64:/opt/intel/composer_xe_2013_sp1.2.144/debugger/gdb/intel64_mic/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/var/cfengine/bin:/opt/gold/bin:/opt/gold/sbin::/usr/java/latest/bin:/opt/maui/bin:/opt/torque/bin:/opt/torque/sbin:/opt/torque/bin:/opt/torque/sbin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/sdsc/bin:/opt/sdsc/sbin:/opt/biotools/bamtools/bin:/opt/biotools/bedtools/bin:/opt/biotools/bismark:/opt/biotools/blast/bin:/opt/biotools/blat/bin/x86_64:/opt/biotools/bowtie/bin:/opt/biotools/bowtie/scripts:/opt/biotools/bowtie2/bin:/opt/biotools/bowtie2/scripts:/opt/biotools/bwa/bin:/opt/biotools/cufflinks/bin:/opt/biotools/edena/bin:/opt/biotools/fastqc:/opt/biotools/fastx/bin:/opt/biotools/gmap_gsnap/bin:/opt/biotools/htseq/bin:/opt/biotools/idba-ud/bin:/opt/biotools/matt/bin:/opt/biotools/miRDeep2/bin:/opt/biotools/miso/bin:/opt/biotools/plink/bin:/opt/biotools/randfold/bin:/opt/biotools/samtools/bin:/opt/biotools/soapdenovo/bin:/opt/biotools/SOAPsnp/bin:/opt/biotools/spades/bin:/opt/biotools/squid/bin:/opt/biotools/tophat/bin:/opt/biotools/trinity/bin:/opt/biotools/trinity:/opt/biotools/velvet/bin:/opt/biotools/ViennaRNA/bin:/opt/biotools/stacks/bin:/opt/biotools/rseqc/bin:/var/cfengine/bin:/opt/gold/bin:/opt/gold/sbin::/opt/maui/bin:/opt/torque/bin:/opt/torque/sbin:/opt/torque/bin:/opt/torque/sbin"

alias fixpaths="export PATH=$PATH_NO_YEO ; export LD_LIBRARY_PATH=$LD_LIBRARY_PATH_NO_YEO"

export PYTHONPATH="$PYTHONPATH:/home/obotvinnik/local/lib/python2.7/site-packages/"

export CSV_FOLDER='/projects/ps-yeolab/obotvinnik/singlecell_pnms/csvs_for_paper'

alias buildgatk='ant clean dist'

# Big friendly repo cleaner for removing large files from github
alias bfg="java -jar $HOME/bin/bfg-1.12.12.jar"

tscc_login_output.txt

Unloading compiler-dependent module boost/1.55.0
Unloading compiler-dependent module gsl/1.16
Unloading compiler-dependent module openmpi_ib/1.8.4
gnu/4.9.2(39):ERROR:105: Unable to locate a modulefile for 'gsl/1.16'
cufflinks/2.2.1(65):ERROR:105: Unable to locate a modulefile for 'boost'
intel/2013_sp1.2.144(64):ERROR:105: Unable to locate a modulefile for 'boost'
intel/2013_sp1.2.144(64):ERROR:105: Unable to locate a modulefile for 'openmpi_ib'
intel/2013_sp1.2.144(64):ERROR:105: Unable to locate a modulefile for 'gsl'
intel/2013_sp1.2.144(64):ERROR:105: Unable to locate a modulefile for 'boost'
[obotvinnik@tscc-login2 ~]$