Tutorial of Running this project (Beta 1)
Prerequest:
OS: Linux 64bit
java: openjdk_1.8.0
maven: 3.3.9
mysql: Ver 15.1 Distrib 10.0.21-MariaDB
blast: 2.4.0+
*Please make sure java, mvn, mysql, blastp are all in your paths.
How to run this project:
Step 1. Init the Database
- Create an empty database schema named as "pdb", username as "cbio", password as "cbio" in mysql:
In mysql prompt,type:
CREATE USER 'cbio'@'localhost' IDENTIFIED BY 'cbio';
GRANT ALL PRIVILEGES ON . TO 'cbio'@'localhost';
FLUSH PRIVILEGES;
create database pdb;
- In your code workspace, git clone https://github.com/cBioPortal/pdb-annotation.git
- Change settings in src/main/resources/application.properties
(i) Change workspace to the input sequences located ${workdir}.
(ii)Change resource_dir to "~/pdb-annotation/pdb/src/main/resources/"
(iii)Change ensembl_input_interval for memory performance consideration
(iv) * If you want to use other test ensembl sequences, please change both ensembl_download_file and ensembl_fasta_file in your workspace
- mvn package
- in pdb-annotation/pdb-alignment-pipeline/target/: java -jar -Xmx7000m pdb-0.1.0.jar init
Step 2. Check the API
- in pdb-annotation/pdb-alignment-api/: mvn spring-boot:run
- Swagger-UI:
http://localhost:8080/swagger-ui.html
- Directly using API:
http://localhost:8080/pdb_annotation/StructureMappingQuery?ensemblId=ENSP00000483207.2
http://localhost:8080/pdb_annotation/ProteinIdentifierRecognitionQuery?ensemblId=ENSP00000483207.2
Step 3. Weekly update
- in pdb-annotation/pdb-alignment-pipeline/target/: java -jar -Xmx7000m pdb-0.1.0.jar update
Notes:
Typical Running time for pipeline Init : 80219.905 Seconds (around 22 hours)
Typical Running time for pipeline Update: 1062.796 Seconds (around 20 minutes)
Test on Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz, 8 cores, 8G Memory
Linux version 3.18.7-200.fc21.x86_64 (gcc version 4.9.2 20141101 (Red Hat 4.9.2-1) (GCC) ) #1 SMP
OpenJDK version "1.8.0_65" 64-Bit Server VM (build 25.65-b01, mixed mode)
mysql Ver 15.1 Distrib 10.0.21-MariaDB, for Linux (x86_64) using EditLine wrapper
Please let me know if you have questions.