https://github.com/remiljw/embl
https://github.com/remiljw/embl
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/remiljw/embl
- Owner: remiljw
- Created: 2021-10-01T21:04:36.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2021-10-07T22:52:42.000Z (over 3 years ago)
- Last Synced: 2025-01-20T12:23:43.131Z (5 months ago)
- Language: Java
- Size: 66.4 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# EMBL
## Project
This repo consists of two projects in two folders, one is a perl script which converts chromomsomes with the [Ensembl API](http://www.ensembl.org/)located in the `ensmbl-perl` folder and the other, a Java(Spring) API to fetch data from two primary tables located in the `ensemble-table-api` folder.
## Software Requirements
To run both of these projects sucessfully, you will need to have some software readily installed on your OS.
#### Requirements for the Java(Spring) Project:
- Java 17 or later. Download [here](https://www.oracle.com/java/technologies/downloads/)
- [Maven](https://maven.apache.org/install.html)
- [PostgreSQL](https://www.postgresql.org/download/)
#### Requirements for the Perl script:
- [Perl](https://www.perl.org/get.html)
- [Ensembl API](http://www.ensembl.org/info/docs/api/)
- There are different guides for setting up the Ensembl API based on your OS:
- [Windows](https://www.ensembl.info/2014/02/10/ensembl-api-on-windows/)
- [Linux](http://www.ensembl.org/info/docs/api/api_installation.html)
- [OSX](https://www.ensembl.info/2013/09/09/installing-perl-dbdmysql-and-ensembl-on-osx/)
- [Using a Virtual Machine](http://www.ensembl.org/info/data/virtual_machine.html)
- If you encountered issues while trying to setup the API, you can check the list of common issues [here](http://www.ensembl.org/info/docs/api/debug_installation_guide.html).
## Run Instructions
### Running the Perl Script
- Clone the project onto your system.
- Launch your terminal and cd into the `ensembl-perl` and run the script with command:
```bash
perl convert_chromosomes.pl
```
### Running the Java(Spring) API
- Start your Postgres server and create a database with any name of your choice.
- Update the `application/proporties` file in the resource directory of the Java project with the database name and Postgres user
```java
spring.datasource.url=jdbc:postgresql://localhost:5432/
spring.datasource.username=
spring.datasource.password=
```
- In your terminal cd into the `ensembl-table-api` folder and run:
```bash
mvn spring-boot:run
```
- You can then visit the url returned at the end of the build in your browser.