Unverified Commit 0dcd6b92 authored by Ankur Kumar's avatar Ankur Kumar
Browse files

Update instructions

- Add example of env file
- Made default location of data file mountings more clear
parent 9ec610fa
......@@ -29,8 +29,8 @@ You can use your custom mine for the builds.
- Set the git url of your mine to the env var `MINE_REPO_URL`. (directory structure similar to biotestmine is assumed)
If you do not have your mine hosted on github/gitlab then you can also mount your mine files directly to the build container. Add your mine folder inside `/data/mine` folder created by docker compose and uncomment the following line in the docker-compose.yml file.
```
If you do not have your mine hosted on github/gitlab then you can also mount your mine files directly to the build container. Add your mine folder inside `./data/mine` folder created by docker compose and uncomment the following line in the docker-compose.yml file.
```bash
# - ./data/mine/[PUT_YOUR_MINE_NAME_HERE]:/home/intermine/intermine/ [PUT_YOUR_MINE_NAME_HERE]
```
......@@ -52,15 +52,24 @@ You can use your custom mine for the builds.
### Adding data and project configs
After quickstart you have a data folder created at your current working directory.
#### Data
After quickstart you have a data folder created at your **current working directory**.
You can also create the folder structure on your own if you do not want to do a quickstart. Create a folder structure like `./data/mine/data`
You can also create the folder structure on your own if you do not want to do a quickstart. Create a folder structure like `data/mine/data`
Add your data files to **`./data/mine/data`** folder and then uncomment the following line in intermine_builder section of your docker-compose file:
```bash
# - ./data/mine/data:/home/intermine/intermine/data
```
Add your data files to **`data/mine/data`** folder. If you do not want to copy your data files over then change location of data files from **`data/mine/data`** folder to your desired folder location in docker-compose.yml file.
If you do not want to copy your data files over then change location of data files in your docker-compose file from **`./data/mine/data`** folder to your desired folder location in docker-compose.yml file.
> Remeber to create a folder for every data source you use. Also make sure that you have appropriate permissions for mounting your data dir to a docker container.
Add your config files to **`data/mine/config`** folder. Configs include your properties file.
#### Configs
Add your config files to **`./data/mine/config`** folder. Configs include your properties file.
> In your properties file, do the following changes:
......@@ -83,7 +92,12 @@ Add your config files to **`data/mine/config`** folder. Configs include your pro
webapp.password=TOMCAT_PWD
### Changing default settings
You can configure a lot of options by creating a .env file in the current working directory and adding the required key value pairs. These are used as env vars by docker-compose.
You can configure a lot of options by creating a `.env` file in the current working directory and adding the required key value pairs. These are used as env vars by docker-compose. For example:
```bash
MINE_NAME=humanmine
MINE_REPO_URL=https://github.com/julie-sullivan/humanmine
IM_DATA_DIR=/tmp/data
```
Available options are:
- MINE_NAME
......@@ -99,7 +113,7 @@ Available options are:
Set it to the data dir prefix that you have in your project.xml file. This will be used for search and replace to fix data locations inside the build container.
> Note: DO NOT add the trailing "/"
- TOMCAT_HOST_PORT
Set the port of your host machine to which tomcat docker container binds to. This is the port that you will use to access the mine webapp.
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