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