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Welcome to the wiki!

These guides are primarily written for use on Linux systems; it may be possible to adapt some procedures to other *NIX systems like macOS with relatively minor changes, but we have not tested these use cases. Installations on Windows will likely be more complicated, and may require various supplementary procedures or compatibility layers.

We recommend something like the following directory hierarchy for ease of housekeeping, and will assume this general structure from now on.

<this-repo>/
├── docs/               <-- picker installation/usage guides
├── patches/
├── pickers/
│   ├── picker1/        ⎤
│   ├── picker2/        ⎥ pickers to be installed here
│   └── picker3/        ⎦
├── demo_data/
│   ├── mrc/
│   ├── train_mrc/
│   ├── train_coord/
│   ├── picker1_out/    ⎤
│   ├── picker2_out/    ⎥ picker output, created in guides
│   └── picker3_out/    ⎦
... etc.

If you haven't already, please clone the most recent version of this repo (which follows the above structure) and change directory into the clone. All installation guides will begin by assuming that your current working directory is the root of this repository. Note that here and in all guides, /path/to/something should be replaced by the path to the indicated resource on your system.

git clone --depth 1 https://github.com/sebseager/cryoem-picker-eval.git && cd cryoem-picker-eval

This repo's demo_data/ directory contains some sample data (five micrographs from the EMPIAR-10017 beta-galactosidase data set) that can be used to test picker installations. All guides will refer to these data, but any references to demo_data/ can be replaced with applicable paths to your own micrograph data.

To get started, take a look at our particle picker usage guides (see table of contents in sidebar).

Additional remarks

Anaconda/Miniconda

Most of these guides assume that the Anaconda package manager (referred to as conda) is available on your system. If not, it can be installed by following these instructions. We recommend using the lighter Miniconda distribution for most applications. A PDF with a list of useful conda commands can be found here.

When switching between different conda environments, we will use conda activate my_environment_name and conda deactivate my_environment_name. This is the preferred method to use with conda versions 4.4.0 and above. A possible exception to this may be shell scripts or cluster job queue scripts, where you may find that the following method works better:

source /path/to/miniconda#/bin/activate /path/to/conda_envs/my_environment_name

If the conda activate or conda deactivate commands do not work, you will need to add the conda executable to your PATH environment variable. To allow conda to run its built-in setup automatically, use

/path/to/miniconda#/bin/conda init

or, to add conda to your PATH temporarily (for your current shell session only), use

export PATH=/path/to/miniconda#/bin:$PATH

or, to add conda to your PATH such that it persists across shell sessions, add it to your ~/.bashrc (or ~/.zshrc, etc. depending on your shell) like so

echo 'export PATH=/path/to/miniconda#/bin:$PATH' >> ~/.bashrc