primelabsms/protein_quantification repository overview

⁠Protein Quantification Containerized

⁠General usage:

docker run --rm -v "$(pwd)":/home/data --env PEPTIDES_FILE=peptides.json --env FASTA_FILE=sequences.fasta primelabsms/protein_quantification

⁠Editing source files and testing in container

If you're editing the cpp source code and wish to mount these source files and test in the container:

docker run -i -t --name edit_code -v "$(pwd)"/data:/home/data -v "$(pwd)"/source_files:/home/source_files primelabsms/protein_quantification /bin/bash

Then you'll have to build the source files again: cd docker mkdir build cd build

• Retrieve json parsing library git clone https://github.com/nlohmann/json/git⁠

• Builds: cmake .. cmake --build .

• Copies executable to home location: cp ProteinQuantification /home

• Test edited source files: ./ProteinQuantification data/peptides.json data/ups.fasta

Note: After these steps, if you continue to edit and test, you don't need to download the json library again

⁠Additional Notes

⁠Resources