Workstations EMBO 2016 - Revision history

Daniel Castaño at 18:03, 29 August 2016

2016-08-29T18:03:44Z

2016-08-29T18:03:29Z

2016-08-29T18:03:11Z

2016-08-29T18:02:04Z

2016-08-25T12:53:30Z

2016-08-25T12:52:51Z

2016-08-25T11:26:41Z

Installing Dynamo

2016-08-25T10:24:07Z

2016-08-25T10:21:31Z

2016-08-25T09:59:21Z

@@ Line 66: / Line 66: @@
 This includes in the linux shell the paths that it needs to find both ''Dynamo'' and its libraries.
-===Running ''Dynamo===
+===Running ''Dynamo''===
 Now, you can just type in the terminal:

@@ Line 1: / Line 1: @@
-== Installing ''Dynamo''==
+EMBL provides a set of Windows laptops. As ''Dynamo'' does not run on Windows, we need to enter a virtual linux environment in the laptop.
 Each participant can have their own ''Dynamo'' installation. The installation procedure needs to be performed only once during the workshop.
@@ Line 14: / Line 47: @@
 <tt>tar -xf <NAME OF THE TAR> -C /g/embo2016/cryo06/dynamo</tt>
-== Activation==
+=== 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.
@@ Line 32: / Line 65: @@
 This includes in the linux shell the paths that it needs to find both ''Dynamo'' and its libraries.
-==Running ''Dynamo==
+===Running ''Dynamo===
 Now, you can just type in the terminal:

← Older revision		Revision as of 12:53, 25 August 2016
Line 41:		Line 41:

	For this workshop, we are using a special version of ''Dynamo'', which will request you to type:		For this workshop, we are using a special version of ''Dynamo'', which will request you to type:
		+
	<tt>modeltrack.format('force',1);</tt>		<tt>modeltrack.format('force',1);</tt>
		+
		+	after the ''Dynamo'' prompt <tt>Dynamo >> </tt>

← Older revision		Revision as of 12:52, 25 August 2016
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	which should open a [[standalone]] console, that can be used to enter ''Dynamo'' commands manually.		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:
		+	<tt>modeltrack.format('force',1);</tt>

@@ Line 4: / Line 4: @@
 Each participant can have their own ''Dynamo'' installation. The installation procedure needs to be performed only once during the workshop.
-Get the tarball from this [[https://drive.google.com/file/d/0B_T9apWxsZjMdTdfd1BFUFNBdkE/view?usp=sharing google drive location]]
+Get the tarball (i.e., <tt>.tar</tt>file)  from this [[https://drive.google.com/file/d/0B_T9apWxsZjMdTdfd1BFUFNBdkE/view?usp=sharing google drive location]]
-We first create a location to install ''Dynamo'', for instance
+We first create a location to install ''Dynamo'', for instance:
 <tt>mkdir /g/embo2016/cryo06/dynamo</tt>
-and then untar the file onto the chosen location
+and then untar (expand) the file onto the chosen location
 <tt>tar -xf <NAME OF THE TAR> -C /g/embo2016/cryo06/dynamo</tt>

@@ Line 1: / Line 1: @@
 In your terminal open a fresh linux shell.
@@ Line 13: / Line 31: @@
 Now, you can activate ''Dynamo'' in the linux shell by running:
-<tt>source ~/tmp/dynamo_activate_linux_shipped_MCR.sh</tt>
+<tt>source /g/embo2016/cryo06/dynamo/tmp/dynamo_activate_linux_shipped_MCR.sh</tt>
 This includes in the linux shell the paths that it needs to find both ''Dynamo'' and its libraries.
 Now, you can just type in the terminal:

@@ Line 5: / Line 5: @@
 <tt>export PATH=/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/programs/share/bin</tt>
-Before starting ''Dynamo'', there is another environment variable that we need to tune.
+<tt>unalias dynamo</tt>
 <tt>export MCR_CACHE_ROOT=~/tmp/</tt>