Using SEASR’s Workbench to Explore the Past, Part Three: Install Guide for Newer Users

There’s been a fair bit of interest in how to use SEASR’s MEANDRE workbench. Installation is a pinch if you’re familiar with setting up a local server and have some fluency on a command line, but if not, I thought I’d give some step-by-step instructions on how to set it up on your own computer. Ideally, you’d install this on a server, but if that’s not an option running it locally is doable.

I am not a technical writer, but if you have a bit of fluency and have patience, this should help you out!

Here are some basic step-by-step instructions for users on OS X (Linux should be pretty similar).

Downloads:
– Oracle Java 1.6+ – http://java.com/en/download
– Scala 2.7.7 – http://www.scala-lang.org/sites/default/files/linuxsoft_archives/downloads/distrib/files/scala-2.7.7.final.zip
– MongoDB – http://www.mongodb.org/downloads
– Meandre-Workbench-1.4 – http://repository.seasr.org/Meandre/Releases/1.4/1.4.11/Meandre-Workbench-1.4.11.jar
– Meandre 2.0 Server – http://repository.seasr.org/Meandre/Releases/2.0/beta2/

I suggest creating a ‘MEANDRE’ directory either in your user directory, or your desktop, and using that to save all of these files. That way you can find them easily if you’re not fluent on the command line.

Setting it all up:
– Install Java. If you’re on OS X, Java should already be installed.

– Set up Scala.

To set up Scala, you need to navigate to your command line interface (it should be in your Applications folder, then Utilities). You need to find the directory that you unzipped SCALA into. Let’s say you downloaded it into your MEANDRE folder, and then unzipped it there.

Open up the command line:

cd --

This brings you back to your user directory. Then let’s go to the Meandre directory.

cd desktop
cd meandre

Then let’s go into the Scala directory, which should by default be scala-2.7.7.final

cd scala-2.7.7.final

Then we need to move into the bin folder and run a command:

cd bin
 chmod +x *

– Set up MongoDB

In your Meandre directory, set up a new directory called ‘mongo-db.’ So it should now be located in /USER/desktop/Meandre/mongo-db.

Now, using your terminal, go into the folder that Mongo was unzipped into. Again, by default, it will be in your MEANDRE folder (you’ll then have to go to the ‘bin’ folder within that). Make sure you change the directory after –dbpath to where you made that database directory!

cd mongodb-osx-i386-2.0.5
cd bin

To run:

./mongod --dbpath=/users/[yourUSERname]/desktop/Meandre/mongo-db

It should now be running. You want to leave that terminal window running, but you can open up a new one.

Here is what my screen looks like, navigating from my basic user directory (which you can always access by typing cd –)

– Setting up the server

Again, you’ve unzipped the server file into this directory. Go in with your folder, and you need to edit the run.sh file in that directory, like so – you can use TextEdit:

In that file, you need to change the SECOND LINE which is SCALA and set it to the path that your scala installation is. For example, my second line now reads:

SCALA=/users/ianmilligan/desktop/meandre/scala-2.7.7.final/bin/scala

Now, to run the server, do the following – make sure you’re in that server directory in your terminal and just type:

./run.sh

To check if it is running, open your browser and navigate to http://localhost:1714/. Password and username will both be ‘admin’.
Again, here is the terminal:

– Setting up the Workbench

– Again, you’ve downloaded the workbench. To run it, you can just actually doubeclick on the jar file that you’ve downloaded, or manually run it from the directory that you downloaded it into. For example, I run this from my Meandre folder.

The command for this is:

java -Xmx1g -jar Meandre-Workbench-1.4.11.jar

You can access the workbench on http://localhost:1712/

Again, here is my terminal from cd — onwards:

SHUTTING IT DOWN

When it comes time to shut it down, or you feel that you can reboot it, you can do this handily. In your terminal window, you can check the processes that are running from the terminal:

Type ps from anywhere:

Now, if you want to shut it down, you can send kill commands. For example, in this instance the following commands would shut everything down:

kill 58717
kill 58723
kill 58735
kill 58742

In the worst case, if something isn’t shutting down, you can always use kill -9 58717 to force it to stop. This isn’t recommended, however, as it may mess with your installation.

AFTER INSTALLATION, HOW DO I RUN IT?

It’s easy from now. You just need to turn them all on the basic way, i.e. the commands (look up above to see where you exactly run them, it will become second nature):

java -Xmx1g -jar Meandre-Workbench-1.4.11.jar

(in your meandre directory)

./run.sh

(in your server directory)

mongod --dbpath=/users/[yourUSERname]/desktop/Meandre/mongo-data

(in the MongoDB BIN directory)

3 thoughts on “Using SEASR’s Workbench to Explore the Past, Part Three: Install Guide for Newer Users

  1. Jim says:

    Thanks Ian, this is great. I’ve installed it on Ubuntu and the instructions generally worked. Two issues. First, I figured I could simply use sudo apt-get to install Scala, but this installed a newer version that does not work with MEANDRE. Follow Ian’s instructions and it will work fine. Secondly, I had problems getting mongodb up and running. The Ubuntu version (installed following instruction on the Mongodb website: http://docs.mongodb.org/manual/tutorial/install-mongodb-on-debian-or-ubuntu-linux/) included a script that started a test database each time I launched the computer and I had to kill that database (which was complicated) before I could run Ian’s command. After lots of searching around I found and deleted the problem, a second mongodb.conf file located the etc/init folder and it and this seems to have solved the problem (leave the main mongodb.conf file in the /etc folder alone; you’ll also need to delete the unwanted database files that take 2-3 gb of disk space). Now I just need to learn how to actually use the workbench.

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