Workstations EMBO 2016

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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


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/

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:


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:


after the Dynamo prompt Dynamo >>