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Overview:
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cd $WORK/src/BioITeam
cp -r /corral-repl/utexas/BioITeam/bin .
cp -r /corral-repl/utexas/BioITeam/python2.7 .
cp -r /corral-repl/utexas/BioITeam/lib .
cp -r /corral-repl/utexas/BioITeam/local .
cp -r /corral-repl/utexas/BioITeam/perl5 .
cp -r /corral-repl/utexas/BioITeam/breseq . |
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Some of these copy commands may take a few minutes to complete (the bin directory specifically) and you may see some permissions errors such as the following. This is expected and not concerning.
cp: cannot open `/corral-repl/utexas/BioITeam/bin/smrtanalysis-2.0.1/analysis/lib/python2.7/networkx-1.1-py2.7.egg/networkx/drawing/nx_pydot.pyc' for reading: Permission denied
When the last of the above commands has finished, copy our predefined GVA2016.bashrc file from the /corral-repl/utexas/BioITeam/scripts/ folder to your $HOME folder as .bashrc before using the chmod command to change the permissions to read and write for the user only.
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