Skip to content

Latest commit

 

History

History
62 lines (49 loc) · 1.98 KB

README.md

File metadata and controls

62 lines (49 loc) · 1.98 KB
Raw

MSTracer -- Now Available on Docker Hub!

MSTracer version 1.1.0

Quick Start

  • Docker download and install docker
  • Run application:
docker run --rm -v $PWD:/app -w /app trackerrr/mstracer java -jar /mstracer/mstracer.jar -mzXML [PATH_TO_MZXML]

Note: Put your .mzXML file in data/ or any designated folder. Your output files will be generated in that folder as well.

In the commands, replace [PATH_TO_MZXML] with the path to your file, or try with a preloaded data toy.mzXML.

The output file isyour-file-name_precursors.tsv.

Developer Usage

Clone & navigate to the repository.

git clone https://github.com/waterlooms/mstracer.git
cd mstracer

Code Setup

Structure at dia_data_reading/ should look like the following:

dia_data_reading/
└───.github/workflows/
└───data/
└───scripts/
└───src/
│   └───main/
│      └───java/edu/uw/waterlooms/
│      └───python/
│      └───resources/
│   └───test/
.dockerignore
.gitignore
Dockerfile
Makefile
docker-compose.yml
pom.xml
README.md
output_file_instruction.txt

Your data files should be located in the data/ folder.
By default, the program will execute on the toy.mzXML file located in mstracer/data/.
JAVA source files should go under mstracer/src/main/java/edu/uw/waterlooms/.
PYTHON source files should go under mstracer/src/main/python/.

Troubleshooting

Note

Should there be any issue with Step 4, another way is to run NN.py using PyCharm.

Right click the "tensorflow" at the third line, choose "Show Context Actions"; choose "install package tensorflow". This sets up a virtual environment that runs Tensorflow.

In the configuration, (1) choose Python from Templates. (2)Set the script path to that of NN.py (e.g.home/Desktop/ms-tracer/src/main/python/NN.py). (3) Parameters should be "-feature data/your-file-name.mzXML"