Installation Guide

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Elaine Ho edited this page Apr 3, 2023 · 5 revisions

Software requirements (external prerequisites)

CUDA 11.3.1
Motioncor2
ctffind
IMOD
AreTomo
miniconda

Obtaining Ot2Rec

Ot2Rec can be obtained by cloning this repository

git clone https://github.com/MasterVexillen/Ot2Rec.git

Installing Ot2Rec

You will need miniconda. If you have not yet installed miniconda yet, you can obtain it by following the instructions here.
(Optional, but recommended) Update miniconda
```
conda update conda
```
Once miniconda is set up, create a virtual environment for Ot2Rec and activate the environment
```
conda create --name o2r
conda activate o2r
```
Go to the Ot2Rec folder and install Ot2Rec
```
cd /path/to/Ot2Rec/
pip install -e .
```

Note that you will need to have a separate installation of the different plugins you'd like to use, e.g., IMOD or AreTomo.

(RFI Users: use module load ... to load the plugins, e.g., module load imod.