This guide will show you how to create a new InterMine. You will need all the dependencies listed in Software.
Note These instructions assume you have taken the Tutorial, a detailed guide to integrating data with InterMine.
See Quick Start to run our test InterMine - BioTestMine.
Download the script.
Execute the script to generate your InterMine instance. Here we are using
TigerMine but of course you would use your mine name here.
You will see a message like:
created /home/$USER/git/tigermine directory for tigermine.
You now have an InterMine! The tutorial goes into detail about the various files that comprise an InterMine.
Your InterMine uses a properties file for database usernames and passwords, let's create that file now.
Make an intermine directory in your home directory.
Copy the properties file you created in the tutorial.
Rename the file to match your Mine.
Now update your new properties files with the values correct for your InterMine. You'll want to update the details for your InterMine databases, you'll create those in the next step.
See Database and Web application for details on this file and what each property means.
Just as in the demo, you will create your InterMine databases.
Note These database names should match the ones you added to your mine.properties file in the previous step.
These databases are empty. We'll populate the main database in the following steps, but let's put some default information in our user database now.
The data loaded into your mine is controlled by the
project.xml file located in the root of your mine directory. See Project XML for an in depth description of this file.
InterMine has a few dozen libraries for popular data sources you can use. See Data Source Library for the full list. Select one of the data sources and add it to your project XML file. Don't forget to download the data too.
For example, NCBI - Entrez gene loads gene information from the NCBI. Download the data files listed, then add the given project XML entry to your own mine's project XML file, like so:
See Writing your own data source if you want to load your own data into your mine.
You can also add "postprocesses" to your build, these are tasks that run after the database build, tasks to build the search index for example. Here are common ones you might want to include:
See Post processing for details on what postprocesses do.
Solr handles the keyword search in InterMine. See Solr for details on how to set Solr up for your mine.
If you skip this step, your mine will work fine but the keyword search will fail.
Now run the build!
project_build script from your
See project_build script for more on the
Your build (depending on your sources) will take a few minutes to run. Once that is done, deploy your webapp. Make sure tomcat is running.
See Gradle - Quick Start for more on Gradle.
Congratulations! You now have an InterMine! Visit it at localhost:8080/tigermine. (replace
tigermine with the name your chose for your mine)
Next you will want to: