This plugin provides a wrapper for Gautomatch picker developed by Kai Zhang at MRC LMB.
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-gautomatchDeveloper’s version
download repository
git clone -b devel https://github.com/scipion-em/scipion-em-gautomatch.gitinstall
scipion installp -p /path/to/scipion-em-gautomatch --devel
Gautomatch binaries will be installed automatically with the plugin, but you can also link an existing installation.
Configuration variables
CONDA_ACTIVATION_CMD: If undefined, it will rely on conda being in the PATH. An example of a conda activation cmd can be eval “$(/extra/miniconda3/bin/conda shell.bash hook)”.
GAUTOMATCH_ENV_ACTIVATION: Command to activate the Gautomatch environment. This environment must have CUDA installed (cudatoolkit=10.1).
GAUTOMATCH_HOME: Path to gautomatch binary containing folder (default = software/em/gautomatch-0.56)
GAUTOMATCH_BIN: Specific binary to use (default = Gautomatch_v0.56_sm30-75_cu10.1)
Verifying
To check the installation, simply run the following Scipion test:
scipion test gautomatch.tests.test_protocols_gautomatch.TestGautomatchAutomaticPicking
Supported versions
0.56
Protocols
References
Kai Zhang. Unpublished.
2 maintainers
Metadata
2 maintainers
Release files for scipion-em-gautomatch 3.2.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scipion_em_gautomatch-3.2.1.tar.gz | 33.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_gautomatch-3.2.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 73.4 kB
Release files / scipion_em_gautomatch-3.2.1.tar.gz
| Download URL | scipion_em_gautomatch-3.2.1.tar.gz |
|---|---|
| Size | 33.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
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Release files / scipion_em_gautomatch-3.2.1-py3-none-any.whl
| Download URL | scipion_em_gautomatch-3.2.1-py3-none-any.whl |
|---|---|
| Size | 39.7 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
0dc77d8d61c934d51d27190dc6f943a171eaea4f63bff2c30671901b700ba2c3
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
|
