Installation

Requirements

BAMTools

Clone the BAMTools repository from GitHub: https://github.com/pezmaster31/bamtools

Compile it on this way and set the environment variables for TPMCalculator:

cd bamtools
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=../ ..
make
make install
cd ..
export BAMTOOLS_DIR=`pwd`
export CPPFLAGS="-I $BAMTOOLS_DIR/include/bamtools/"
export LDFLAGS="-L $BAMTOOLS_DIR/lib64 -Wl,-rpath,$BAMTOOLS_DIR/lib64"

That's it. BAMTools was compiled and the env variables were set for compiling TPMCalculator.

Installation

After the installation of BAMTools go to the TPMCalculator folder and do make:

make

A bin folder will be created with the TPMCalculator executable.

Docker

Use provided Dockerfile based on the BioContainers base image.

docker build -t biocontainers/tpmcalculator:0.0.1 https://raw.githubusercontent.com/ncbi/TPMCalculator/master/Dockerfile

docker run -v /path_to_data:/data --user=yourUID:your:GID biocontainers/tpmcalculator:0.0.1 TPMCalculator -g /data/path_to_GTF/genes.gtf -b /data/path_to_bam/sample1.bam

CWL

A CWL tool definition is also provided tpmcalculator.cwl

Use it like this:

cwl-runner tpmcalculator.cwl --out_stderr=test.stderr --out_stdout=test.stdout -g genes.gtf -b sample_1.bam