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SETUP.md

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Reference Data

A list of data that need to be installed

Directory setup

# This will store reference datasets.
mkdir -p /export/refs

# This will store source code not installed through conda.
mkdir -p /export/src

# Link executables into this directory.
mkdir -p /export/bin

Centrifuge

DIR=/export/refs/centrifuge/
mkdir -p $DIR
(cd $DIR && curl -O ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz)
(cd $DIR && tar xzvf p_compressed+h+v.tar.gz)

Augustus

DIR=/export/src/
mkdir -p $DIR
(cd $DIR && curl -O http://bioinf.uni-greifswald.de/augustus/binaries/augustus.current.tar.gz)
(cd $DIR && tar xzvf augustus.current.tar.gz)
sudo apt-get install bamtools libbamtools-dev
(cd $DIR/augustus && make)

then one of:

#
#(cd $DIR/augustus && sudo make install)
#
# Alternatively link each required executable.
#ln -fs $DIR/augustus/bin/augustus /export/bin
# ln -fs $DIR/augustus/bin/augustus /export/bin