View source for Scripted creation of a project in the Linux command line

It is possible to fully run ''Dynamo'' outside of Matlab AND the ''Dynamo'' [[standalone]], as described [[ standalone#For independent commands | here]]

Here we show how to create from scratch a project. This assumes that you already have a [[data folder]], a [[table]],a  template, and several  masks (for [[Alignment mask|alignment]], classification, description of fourier content of template and [[Smoothing mask|smoothing while FSC computing]]). If you don't you can just run (in the linux shell) the command: 

 <tt>dynamo 'dynamo_tutorial ttest'</tt>

(This is equivalent to opening an interactive ''Dynamo'' [[Dynamo console| console]], waiting for it to open, and then typing <tt>dutorial ttest</tt> in it). This command just creates some example files for data, etc, which we can use now to show how they can be linked into a project.

We then create a single script where we write all the commands that we would use interactively to create a project. Use any editor in your system to open a file, let's  call it <tt>createProject.sh</tt>, and type the lines:

 <pre>
dynamo_vpr prtest
dynamo_vpr_put prtest -data ttest/data
dynamo_vpr_put prtest -template ttest/template.em
dynamo_vpr_put prtest -table ttest/initial.tbl
dynamo_vpr_put prtest -mask ttest/mask.em
dynamo_vpr_put prtest -cmask ttest/mask.em
dynamo_vpr_put prtest -fmask ttest/fmask.em
dynamo_vpr_put prtest -smask ttest/mask_smoothing.em
dynamo_vpr_put prtest -ite_r1 2
dynamo_vpr_put prtest -ca_r1 360
dynamo_vpr_put prtest -cs_r1 45
dynamo_vpr_put prtest -dim_r1 32
dynamo_vpr_put prtest -destination standalone
dynamo_vpr_put prtest -cores 2
dynamo_vpr_check prtest
dynamo_vpr_unfold prtest
</pre>

Here, we are just indicating a minimum amount of input that you need to create a working project, which we arbitrarily called <tt>prtest</tt>. We cannot use the short names of the commands in this kind of scripts, i.e., we need to write out <tt>dynamo_vpr_put</tt> instead of <tt>dvput</tt>. To get a list of all project parameters that can be changed with <tt>dvput</tt>, just type the command <tt>dvhelp</tt>.

Now, you can run this script in a Linux shell (provided you have [[ standalone#Activating the standalone  | activated]]  ''Dynamo'' in it) by

 <tt> dynamo createProject.sh </tt>

After that, you can just execute the project by writing:

 <tt>./prtest.exe</tt>