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:

scipion3 install --help

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

Checking plugin updates

scipion3 install --checkUpdates

Listing plugin binaries

This will show the available binaries for our installed plugins:

scipion3 installb --help

Installing

Installing plugins

To install one of the plugins from the list run the install command with the name of the package. For example, to install Relion using 5 processors:

scipion3 install -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:

scipion3 installp -p scipion-em-xmipp -j 5 -p scipion-em-relion -j 5 -p scipion-em-cistem

Install plugin without binaries

You can install a plugin and its binaries in two steps. For this, first we install the plugin without binaries, recommended for HPC clusters or when you already have the binary installed and look at Linking existing software page.:

scipion3 install -p scipion-em-relion --noBin

Tip

The command above is just installing the pip package scipion-em-relion.

scipion3 pip install scipion-em-relion

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 git@github.com:scipion-em/scipion-em-relion.git

Now we should have the plugin in ~/scipion-em-relion. We can install in devel mode by pointing the path after the -p flag:

scipion3 install -p ~/scipion-em-relion --devel

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

Installing binaries

By default installing a plugin very likely will install the binary/s the plugin integrates. Unless you have set de variable SCIPION_DONT_INSTALL_BINARIES either in the environment or in the config file.

Install specific binaries

We list all available binary versions:

scipion3 installb

This should show something like:

[. . . ]
Example: scipion3 installb cistem relion-3.1

Available binaries: ([ ] not installed, [X] seems already installed)
chimerax                 1.0     [X]
cistem                   1.0.0-beta[X]
cryolo                   1.6.1   [X]
cryolo_model             201910  [ ]     202002_N63[X]
cryolo_negstain_model    20190226[ ]
ctffind4                 4.1.13  [ ]
deepLearningToolkit      0.2     [X]
dynamo                   1.146   [X]
eman                     2.3     [ ]     2.31    [X]     3.0.0-alpha[X]
gautomatch               0.53    [ ]     0.56    [X]
gctf                     1.06    [ ]     1.18    [X]
imod                     4.10.42 [X]
janni_model              20190703[ ]
maxit                    10.1    [X]
motioncor2               1.2.3   [ ]     1.2.6   [ ]     1.3.0   [ ]     1.3.1   [X]     1.3.2   [X]
relion                   3.0     [ ]     3.1.0   [ ]
resmap                   1.95    [X]
xmippSrc                 3.20.07b1[ ]

Now we can install our preferred binaries:

scipion3 installb relion-3.1 -j 5