module load cmake/3.5.0
 
 
cd /sw/bioinformatics
git clone https://github.com/domibel/IonTorrent-VariantCaller.git
cd /sw/bioinformatics/IonTorrent-VariantCaller/git
BASE=/sw/bioinformatics/IonTorrent-VariantCaller
TVC_SOURCE_DIR=$BASE/IonTorrent-VariantCaller
TVC_BUILD_DIR=$BASE/IonTorrent-VariantCaller-build
TVC_INSTALL_DIR=$BASE/IonTorrent-VariantCaller-install/usr/local
 
mkdir -p $TVC_BUILD_DIR
mkdir -p $TVC_INSTALL_DIR

cd $TVC_BUILD_DIR
wget --no-clobber updates.iontorrent.com/updates/software/external/armadillo-4.600.1.tar.gz
tar xvzf armadillo-4.600.1.tar.gz
cd armadillo-4.600.1/
sed -i 's:^// #define ARMA_USE_LAPACK$:#define ARMA_USE_LAPACK:g' include/armadillo_bits/config.hpp
sed -i 's:^// #define ARMA_USE_BLAS$:#define ARMA_USE_BLAS:g'     include/armadillo_bits/config.hpp
cmake .
make -j4
 
 
cd $TVC_BUILD_DIR
wget --no-clobber updates.iontorrent.com/updates/software/external/bamtools-2.4.0.20150702+git15eadb925f.tar.gz
tar xvzf bamtools-2.4.0.20150702+git15eadb925f.tar.gz
mkdir bamtools-2.4.0.20150702+git15eadb925f-build
cd bamtools-2.4.0.20150702+git15eadb925f-build
cmake ../bamtools-2.4.0.20150702+git15eadb925f -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo
make -j4

cd $TVC_BUILD_DIR
wget --no-clobber --no-check-certificate https://github.com/samtools/htslib/archive/1.2.1.tar.gz -O htslib-1.2.1.tar.gz
tar xvzf htslib-1.2.1.tar.gz
ln -s htslib-1.2.1 htslib # for samtools
cd htslib-1.2.1
make -j4

cd $TVC_BUILD_DIR
wget --no-clobber --no-check-certificate https://github.com/samtools/samtools/archive/1.2.tar.gz -O samtools-1.2.tar.gz
tar xvzf samtools-1.2.tar.gz
cd samtools-1.2
make -j4
mkdir $TVC_INSTALL_DIR/bin
cp samtools $TVC_INSTALL_DIR/bin/

cd $TVC_BUILD_DIR
mkdir TVC-build
cd TVC-build
cmake $TVC_SOURCE_DIR -DCMAKE_INSTALL_PREFIX:PATH=$TVC_INSTALL_DIR -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo
make -j4 install

*** quick test ***
TVC_ROOT_DIR=$TVC_INSTALL_DIR
$TVC_ROOT_DIR/bin/variant_caller_pipeline.py \
    --input-bam       $TVC_ROOT_DIR/share/TVC/examples/example1/test.bam \
    --reference-fasta $TVC_ROOT_DIR/share/TVC/examples/example1/reference.fasta \
    --region-bed      $TVC_ROOT_DIR/share/TVC/examples/example1/test_merged_plain.bed \
    --primer-trim-bed $TVC_ROOT_DIR/share/TVC/examples/example1/test_unmerged_detail.bed

*** export PATH, following tools are required: samtools zip tvc ***
export PATH=$PATH:$TVC_ROOT_DIR/bin