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How to install
The easiest way to use Localized Reconstruction is from the Scipion GUI. This is available from version 1.1. First find the latest localrec package that has been bundled with Scipion:
./scipion install --help
Then install it, together with Relion 1.4, which is required. For example:
./scipion install --no-xmipp localrec-1.2.0 relion-1.4
Finally make sure that the required packages are in your ~/.config/scipion/scipion.conf file.
LOCALREC_HOME = %(EM_ROOT)s/localrec-1.2.0
LOCALREC_RELION_HOME = %(EM_ROOT)s/relion-1.4
Version 1.2.1 contains important bug fixes to reach high resolution. To upgrade manually to this version please follow these instructions.
Note that these instructions refer to creating a standalone installation for command-line use which is generally not recommended.
Go to the directory where you want to install Localized Reconstruction, and clone it from GitHub (first install git if not present in your system):
git clone https://github.com/OPIC-Oxford/localrec.git
cd localrec
Git will create a localrec/ directory under your current path; you do not need to create it manually.
Then add /localrec/lib in your PYTHONPATH. How to do this depends on your operating system and its configuration.
For Bash shell, add something like this to your .bashrc file (or .bash_profile). Here it is assumed that ~/apps is the install location:
PYTHONPATH=~/apps/localrec/lib
export PYTHONPATH
If you're using C shell, add something like this to your ~/.cshrc
setenv PYTHONPATH ~/apps/localrec/lib
Install Scipion (release-1.1) from https://github.com/I2PC/scipion and follow the instructions to install Relion.
To update the package, just download the latest version from GitHub:
git pull