configure

#!/bin/sh

# configure.sh
# ------------
# used to configure FASTCLIP pipeline

# 1. Checking for dependencies

if $(type bowtie2 >/dev/null 2>&1); then
	echo "bowtie2 installed"
else 
	echo >&2 "bowtie2 must be installed.  Aborting."; exit 1
fi

if $(type STAR >/dev/null 2>&1); then
	echo "STAR installed"
else 
	echo >&2 "STAR must be installed.  Aborting."; exit 1
fi

if $(type fastx_quality_stats >/dev/null 2>&1); then
	echo "FASTX-toolkit installed"
else 
	echo >&2 "fastx_toolkit must be installed.  Aborting."; exit 1
fi

if $(type iCLIPro >/dev/null 2>&1); then
	echo "iCLIPro installed"
else 
	echo >&2 "iCLIPro must be installed.  Aborting."; exit 1
fi

if $(type bedtools >/dev/null 2>&1); then
	echo "bedtools installed"
else 
	echo >&2 "bedtools must be installed.  Aborting."; exit 1
fi

if $(type python >/dev/null 2>&1); then
	echo "python installed"
else
	echo >&2 "python must be installed.  Aborting."; exit 1
fi

if $(python -c "import matplotlib" &> /dev/null); then
	echo "matplotlib installed"
else
    echo >&2 "matplotlib must be installed in python. Aborting."; exit 1
fi

if $(python -c "import pandas" &> /dev/null); then
	echo "pandas installed"
else
    echo >&2 "pandas must be installed in python. Aborting."; exit 1
fi

# 2. Downloading genome files

echo "Downloading and unzipping hg19 and mm9 genome files"
wget https://s3.amazonaws.com/changlabguest/FAST-iCLIP/docs_new.tar.gz
mkdir docs
tar xvzf docs_new.tar.gz -C docs && rm -f docs_new.tar.gz

# 3. Downloading example files
wget https://s3.amazonaws.com/changlabguest/FAST-iCLIP/rawdata.tar.gz
mkdir rawdata
tar xvzf rawdata.tar.gz -C rawdata && rm -f rawdata.tar.gz
mkdir results