# This can be used as an executable to install all dependencies:

# ./INSTALL

# Initialize the conda environment.

conda create -y -n SPURF

source activate SPURF

mkdir -p $CONDA_PREFIX/etc/conda/activate.d

mkdir -p $CONDA_PREFIX/etc/conda/deactivate.d

printf '#!/bin/sh\n\nexport PYTHONNOUSERSITE=1' > $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh

printf '#!/bin/sh\n\nunset PYTHONNOUSERSITE' > $CONDA_PREFIX/etc/conda/deactivate.d/env_vars.sh

source activate SPURF

# Install conda environment:

conda install -y biopython cmake gsl openblas pandas psutil pysam scons seaborn

pip install colored-traceback dendropy==3.12.3

# Install partis for inferring VDJ annotation and naive sequence:

cd partis

./bin/build.sh

cd ..

# Install more conda environment (post partis install b/c this interferes with gcc):

source activate SPURF

conda install -y -c biocore mafft

conda config --add channels r

conda config --add channels bioconda

conda update pysam

conda install -y pyyaml

conda install -y -c r r-base r-rcpparmadillo

# R modules to install:

R CMD BATCH modules2install.R

# Install ANARCI for making AHo annotations:

cd ANARCI_KD_copy

python setup.py install

cd ..

# Running a test:

Rscript --vanilla run_SPURF.R CGCAGGACTGTTGANGCCTTCGGAGACCCTGTCCCTCACCTGCGTTGTCTCTGGCGGGTCCTTCAGTGATTACTACTGGAGCTGGATCCATCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGGAGCACCAACTACAACCCGTCCCTCGAAAGTCGAGCCACCATATCAGTAGACACGTCCCAGAACAACCTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACTCGGCTGTGTATTACTGTGCGAGAGGCCCGACTACAATGGCTCACGACTTTGACTACTGGGGCCAGGGAACCCTGGTCACC seqXYZ_SPURF_output l2