Workstations EMBO 2016

Installing Dynamo

Each participant can have their own Dynamo installation. The installation procedure needs to be performed only once during the workshop.

Get the tarball (i.e., .tarfile) from this [google drive location]

We first create a location to install Dynamo, for instance:

mkdir /g/embo2016/cryo06/dynamo

and then untar (expand) the file onto the chosen location

tar -xf <NAME OF THE TAR> -C /g/embo2016/cryo06/dynamo

Activation

After installing the software, you'll need to activate it on each new shell in which you want to use it. Whenever you open a fresh shell, we need to ensure we have a fresh environment. This means, we need to overrule some default settings that are used by default in the course computers.

export PATH=/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/programs/share/bin

unalias dynamo

Before starting Dynamo, there is another environment variable that we need to tune: MCR_CACHE_ROOT

export MCR_CACHE_ROOT=~/tmp/

Now, you can activate Dynamo in the linux shell by running:

source /g/embo2016/cryo06/dynamo/tmp/dynamo_activate_linux_shipped_MCR.sh

This includes in the linux shell the paths that it needs to find both Dynamo and its libraries.

Running Dynamo

Now, you can just type in the terminal:

dynamo

which should open a standalone console, that can be used to enter Dynamo commands manually.

For this workshop, we are using a special version of Dynamo, which will request you to type:

modeltrack.format('force',1);

after the Dynamo prompt Dynamo >>