tools for adding mutations to .bam files, used for testing mutation callers
Please see doc/Manual.pdf for instructions and contact adam.ewing@gmail.com with questions.
python setup.py build
python setup.py install
The following presumes $HOME/bin is in your $PATH
Samtools / BCFTools / wgsim:
git clone https://github.com/samtools/htslib.git
make -C htslib
git clone https://github.com/samtools/samtools.git
make -C samtools
cp samtools/samtools $HOME/bin
cp samtools/misc/wgsim $HOME/bin
git clone https://github.com/samtools/bcftools.git
make -C bcftools
cp bcftools/bcftools $HOME/bin
BWA (or another aligner, currently supported aligners include bwa, novoalign, gsnap, bowtie2, and tmap)
git clone https://github.com/lh3/bwa.git
make -C bwa
cp bwa/bwa $HOME/bin
Picard tools
wget https://github.com/broadinstitute/picard/releases/download/1.131/picard-tools-1.131.zip
unzip picard-tools-1.131.zip
Exonerate
git clone https://github.com/adamewing/exonerate.git
cd exonerate
git checkout v2.4.0
autoreconf -i
./configure && make && make check && make install
Velvet
wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
tar xvzf velvet_1.2.10.tgz
make -C velvet_1.2.10
cp velvet_1.2.10/velvetg $HOME/bin
cp velvet_1.2.10/velveth $HOME/bin
Pysam
pip install cython
pip install pysam
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh # python3
bash miniconda.sh # install & add conda to your PATH
source ~/.bashrc
conda update -y conda # update conda
conda env create -n bamsurgeon -f environment.yaml # create env & install dependencies
conda activate bamsurgeon
python setup.py install