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module load cmake/3.5.0 cd /sw/bioinformatics git clone https://github.com/domibel/IonTorrent-VariantCaller.git cd /sw/bioinformatics/IonTorrent-VariantCaller BASE=`pwd` #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 $TVC_BUILD_DIR mkdir TVC-build cd TVC-build cmake#cmake /sw/bioinformatics/IonTorrent-VariantCaller/git -DCMAKE_INSTALL_PREFIX:PATH=$TVC_INSTALL_DIR -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo #cmakecmake $TVC_SOURCE_DIR -DCMAKE_INSTALL_PREFIX:PATH=$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 |
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