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vre_app_3dshaper

https://github.com/mapoferri/vre_app_3dshaper

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.5%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: mapoferri
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Size: 16.1 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 3 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License Citation

README.md

VRE Tool Executor for 3D Shaper

Documentation Status

Tool ready to run in the VRE matching the code in the documentation.

Starting from the template for a VRE Tool, this is the adaptation for the 3D Shaper - 3D Simulation Intervertebral Disc workflow.

Requirements

  • Python 3.6 or later
  • Conda env
  • PyTorch
  • PyTorch3D
  • Git

Installation

Directly from GitHub:

bash cd $HOME git clone https://github.com/inab/mapoferri/vre_app_3dshaper.git cd vre_app_3dshaper

Create the Conda environment (attention to changing the paths accordingly):

bash source /anaconda3/etc/profile.d/conda.sh conda env create -f environment.yml

It may be possible to download/update the OpenVRE API directly in the Conda ENV:

bash pip install git+https://github.com/inab/openvre-tool-api.git

Or:

bash pip install -r requirments.txt

Run the Wrapper

bash ./VRE_RUNNER --config tests/basic/config.json --in_metadata tests/basic/in_metadata.json --out_metadata out_metadata.json --log_file VRE_RUNNER.log

Look for the results in tests/basic/run000/.

To test the applications, all the attemps were made from the test/basics dir. To replicate them, access directly the directory.

bash ./test_VRE_RUNNER.sh

License

  • © 2020-2022 Barcelona Supercomputing Center (BSC), ES

Licensed under the Apache License Version 2.0, see the file LICENSE for details.

Owner

  • Name: Maria Paola Ferri
  • Login: mapoferri
  • Kind: user
  • Company: @bsc

Citation (CITATION.cff) 

authors:
  - family-names: Rodríguez-Navas
    given-names: Laura
    orcid: "https://orcid.org/0000-0003-4929-1219"
  - family-names: Codó Tarraubella
    given-names: Laia
    orcid: "https://orcid.org/0000-0002-6797-8746"
cff-version: 1.2.0
date-released: "2020-01-27"
keywords:
  - template
  - wrapper
  - tool
  - vre
license: Apache-2.0
message: "If you use this software, please cite it using these metadata."
repository-code: "https://github.com/inab/vre_template_tool"
type: software
title: "VRE template Tool Executor"
version: 0.1.2

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Dependencies

docs/requirements.txt pypi
  • openvre-tool-api master
  • sphinx *
  • sphinx-automodapi *
  • sphinx-rtd-theme *
requirements.txt pypi
  • openvre-tool-api v0.5.5
vre_template_tool.egg-info/requires.txt pypi
  • openvre-tool-api *
Dockerfile docker
  • python 3.8 build
conda_env/environment.yml pypi
setup.py pypi