Plugin to use AreTomo program within the Scipion framework
Project description
This plugin provide a wrapper around AreTomo program.
prod: |
devel: |
Installation
You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:
Stable version
scipion installp -p scipion-em-aretomo
Developer’s version
download repository
git clone https://github.com/scipion-em/scipion-em-aretomo.git
install
scipion installp -p path_to_scipion-em-aretomo --devel
AreTomo binaries will be installed automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/aretomo-1.0.6, if you want to change it, set ARETOMO_HOME in scipion.conf file to the folder where the AreTomo is installed. Depending on your CUDA version you might want to change the default binary from AreTomo_1.0.6_Cuda101 to a different one by explicitly setting ARETOMO_BIN variable. If you need to use CUDA different from the one used during Scipion installation (defined by CUDA_LIB), you can add ARETOMO_CUDA_LIB variable to the config file. Various binaries can be downloaded from the official UCSF website.
To check the installation, simply run the following Scipion test:
scipion test aretomo.tests.test_protocols_aretomo.TestAreTomo
Supported versions
1.0.6
Protocols
tilt-series align and reconstruct
Detailed manual can be found in software/em/aretomo-1.0.6/bin/AreTomoManual-06-24-2021.pdf
References
Shawn Zheng, unpublished.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Hashes for scipion-em-aretomo-3.0.0b1.tar.gz
Algorithm | Hash digest | |
---|---|---|
SHA256 | 4b81d2c7f93379e822ec7074e23d3f5f9eb42e782ce54edc64453948904c9064 |
|
MD5 | b25a8c6a6e7ce2d10b341136cdcb2008 |
|
BLAKE2b-256 | ee0edf90e9da96ebf4f3922511ba8d42e42f1e8a6739e9452ba23add2b28c0eb |