autorec

A program to automate cryoET image reconstruction under DLS workflow

Installation

1. Git clone repo

git clone https://github.com/MasterVexillen/autorec.git
cd autorec

2. Create virtual environment in miniconda and pre-install packages

conda create -n autorec-env
conda activate autorec-env
conda install --file requirements.txt

3. Build autorec

python setup.py develop

Running autorec

1. Activate autorec environment and load imod

conda activate autorec-env
module load imod

2. Run autorec

autorec.TASK

where TASK can be:

• check: Performs check on prequisite files and folder structure.
• new: Prepares and flips gain reference files, prepares new input parameter file, then modifies the parameters according to user preferences.
• run: Performs a hard check on prerequisite files and folder structure, then runs preprocessing using a user-specified parameter file.