Developer guide: Installing plugins from the command line

This guide contains examples to show the different options available to install and uninstall plugins and their binaries.

Listing

Listing plugins

You can see the up-to-date list of available plugins with this command:

./scipion installp --help

This will also show the instructions to use the installp command line tool.

Checking plugin updates

 scipion installp --checkUpdates

Listing plugin binaries

This will show the available binaries for our installed plugins:

scipion installb --help

Installing

Installing plugins

Devel mode

Installing a plugin in devel mode is handy to make changes to the plugin locally and test them in Scipion immediately. Let's use relion as an example. First, we clone the repo, for example in our home ( ~ ):

git clone [email protected]:scipion-em/scipion-em-relion.git

Now we should have the plugin in ~/scipion-em-relion. We can install in devel mode with the command:

scipion installp -p ~/scipion-em-relion --devel

Changes made to the plugin should now be available when you launch Scipion.

Regular install

To install one of the plugins from the list (by default, all plugins are installed in software/lib/python2.7/site-packages and their binaries in software/em), run the install command with the name of the package. For example, to install Relion using 5 processors:

./scipion installp -p scipion-em-relion -j 5

You may replace -j 5 by the number of cores available in your machine or remove it altogether if you only wish to use one (will be slow). You can also install multiple packages with a single install command:

./scipion installp -p scipion-em-xmipp -j 5 -p scipion-em-relion -j 5 -p scipion-em-grigoriefflab

Installing binaries

Install plugin without binaries

You can install a plugin and its binaries in two steps. For this, first we install the plugin without binaries:

./scipion installp -p scipion-em-relion -j 5 --noBin

Install specific binaries

We list all available binary versions:

./scipion installb --help

This should show something like:

[. . . ]
Example: /home/yaiza/git/scipion/scipion installb ctffind4 unblur-1.0.15

Available binaries: ([ ] not installed, [X] seems already installed)
	         relion       1.4 [ ]     1.4f [ ]      2.0 [ ]      2.1 [ ]      3.0 [ ]
	       xmippBin   3.18.08 [ ]
	       xmippSrc   3.18.08 [ ]

Now we can install our preferred binaries:

scipion installb relion-2.1 -j 5