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pinet-server

http://pinet-server.org

To compile and run

gradle clean build

java -jar build/libs/*.jar

Three main comments:

1- For deepPhos prediction, pinet is listening to port 5000

The file to change that is in /src/main/resources/application.yml

deepPhosUrl: http://localhost:5000/api/predict/organism/%s/%s

2- pinet reads indexed protein files from this folder:

/opt/raid10/genomics/behrouz/PeptideMatchCMD_src_1.0/jan-30-2019/

To change that, whatever is in this folder should be copied to the new folder and the following file should be changed as well:

/src/main/java/edu.uc.eh/peptideMatch/PeptideMatchCMD.java

3- The usage submission increment file is in the /opt/raid10/genomics/behrouz/PeptideMatchCMD_src_1.0/increment.json

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