Installation

Legacy vs modern installations

BeeDeeM software development started in early February 2007. To provide a multi-OS, open source and free software installer at that time, the Apache Ant tool was chosen. This is called the legacy BeeDeeM installer.

Over time, modern installation procedures were provided relying on Conda, Docker and Singularity.

Conda

You can install and run BeeDeeM using Anaconda tool as explained in this documentation. You can benefit from all BeeDeeM features, including the UiInstaller.

Docker

You can run BeeDeeM within a Docker container, as explained in this documentation.

• Pros of Docker configuration: direct use.

• Cons of Docker:

  • not always easy to use on particular clusters,

  • benefit from all BeeDeeM features, but the UiInstaller.

Singularity

You can run BeeDeeM within a Singularity container, as explained in this documentation.

• Pros of Singularity configuration: direct use.

• Cons of Singularity:

  • benefit from all BeeDeeM features, but the UiInstaller.

Legacy installation: Antstaller

You can install the software directly on a computer (or server, or cluster, ...) to benefit from ALL its features, including the use of the UiInstaller. The following section explains how to do that using the Apache Ant installer script (aka Anstaller) provided with BeeDeeM.

We consider an installation on a Unix-based system (Linux, macOS), but you can easily adapt for Windows OS.

BeeDeeM sofwtare installer bundle is available on Github here. There, retrieve the latest beedeem-x.y.z-distrib.zip file (where x.y.z is a version number) which contains the entire BeeDeeM system.

Then proceed as follows:

-1- Prepare a temporary directory from which the installation will be performed:

cd /tmp
mkdir dbms
cd dbms

place the beedeem-x.y.z-distrib.zip file in the directory /tmp/dbms.

-2- Decompress the file beedeem-x.y.z-distrib.zip:

unzip beedeem-x.y.z-distrib.zip

-3- Check if Oracle Java is available on your system:

java -version
   java version "1.8.0_45"
   Java(TM) SE Runtime Environment (build 1.8.0_45-b14)
   Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode)

If Java is already installed and available on your system, jump to step 4, below.

If Java is not available, please proceed to the web site of Oracle to install the Java Runtime Environment. DO NOT use OpenJDK, gcj, etc. BeeDeeM only works well with the original Oracle Java.

-4- Decompress the Ant system supplied with BeeDeeM:

cd ant
unzip  ant-1.9.4.zip
cd bin
chmod a+x ant antRun
cd ../..

-5- Declare your system configuration to install BeeDeeM

You have now to define:

• the directories used by the BeeDeeM installer to correctly deploy it on your system (c.f. Directory structure):

  • installation directory: where BeeDeeM will be deployed,

  • working directory: where BeeDeeM can create temporary files,

  • bank installation directory: where BeeDeeM will install banks;

• the memory parameters to use with JRE.

To do that, edit the file config.properties. This contains documentation explaining how it should be modified.

vi config.properties [update file as needed]

installDir=/opt/beedeem          <-  Installation directory
workingDir=/var/beedeem          <-  Working directory
biobaseRootDir=/biobase          <-  Where to install databases
javaArgs=-Xms128M -Xmx1024M      <-  JRE memory settings

(After editing, save config.properties file)

CAUTION: have in mind that during installation, directories targeted by installDirwill be DELETED (only if they exist) then created by the software installer; e.g. in the above example, /opt/beedeem is deleted then created again by BeeDeeM installer.

It is worth noting that all these values can be updated after installation, but in a less easier way. So carefully choose your installation directories by now.

-6- It is now time to install BeeDeeM using this very simple command:

ant -f deploy.xml install

On start-up, the BeeDeeM installer will ask you to verify your system configuration:

Buildfile: deploy.xml install: [echo] *** PLEASE VERIFY *** [echo] [echo] [echo] Current configuration is: [echo] Installation dir: /opt/beedeem [echo] Working dir : /var/beedeem [echo] BioBase dir : /biobase [echo] Java args : -Xms128M -Xmx4G [input] If ok, press Return key to start the installation...

Do not omit this step: this is the last time you can perform this verification.

In the case of an error, you can interrupt the installation with CTRL+C. Otherwise, continue with this procedure.

Carefully check the final message from Ant. If everything is correct, you should see the message:

 BUILD SUCCESSFUL

-7- Update PATH variable

To ensure easy use of BeeDeeM main command (called bdm), update PATH variable; e.g. on Linux/macOS: export PATH=/path/to/beedeem-installation:$PATH

Note: replace '/path/to/beedeem-installation' by the appropriate path you use during YOUR installation (e.g. it is /opt/beedeem in our exemple).

-8- Finally, try getting BeeDeeM help from the command line:

bdm --help

Or run a full test:

test_bdm