MSTracer version 1.1.0
- 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
.
Clone & navigate to the repository.
git clone https://github.com/waterlooms/mstracer.git
cd mstracer
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/.
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"