scipion-install

Utility script and files to smoothly install Scipion on Linux/MacOS.

NO COMPILATION REQUIRED!!!

It will download a Miniconda installer and install core plugins and some EM plugins. It will also ensure compatibility in library versions with previously compiled Xmipp binary.

Additionally, EMHub will be also installed.

Requirements

• git to clone install repository and other plugins
• python to run the install script

Installing Scipion

It should be very easy to install Scipion following these steps. Just be patient for conda to resolve dependencies and environment libraries. Installation should not require any admin privileges in your computer or compiler tools.

Replace SCIPION_FOLDER in the following command with the path where you want to install Scipion.

git clone https://github.com/delarosatrevin/scipion-install.git
cd scipion-install
python ./install.py SCIPION_FOLDER

After this, you should have a basic Scipion 3.0 installation in SCIPION_FOLDER. You can load the Scipion environment by:

source SCIPION_FOLDER/bashrc

Then you can install some binaries to work with:

scipion installb cistem cryolo cryolo_model ctffind4 gctf motioncor2

It is recommended that you install Relion separately and then link it in the EM folder:

cd SCIPION_FOLDER/EM
ln -s RELION_4.0_FOLDER relion-4.0

And then run some tests to validate the installation:

scipion test [UPDATE]

Development installation

A development installation is very similar that the previous one, since it install the plugins from the source code. Just pass **--git_clone ssh* to use that method for cloning from GitHub. The installation command will be:

python ./install.py SCIPION_FOLDER --git_clone ssh

Xmipp binaries

Xmipp binaries used in the installation are pre-built and hosted in the following repository:

https://github.com/delarosatrevin/xmipp-binaries