Scripted creation of a project in the Linux command line
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, classification, description of fourier content of template and smoothing while FSC computing). If you don't you can just run (in the linux shell) the command:
dynamo 'dynamo_tutorial ttest'
(This is equivalent to opening an interactive Dynamo console, waiting for it to open, and then typing dutorial ttest 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 createProject.sh, and type the lines:
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
Here, we are just indicating a minimum amount of input that you need to create a working project, which we arbitrarily called prtest. We cannot use the short names of the commands in this kind of scripts, i.e., we need to write out dynamo_vpr_put instead of dvput. To get a list of all project parameters that can be changed with dvput, just type the command dvhelp.
Now, you can run this script in a Linux shell (provided you have activated Dynamo in it) by
After that, you can just execute the project by writing: