Cloned from https://github.com/inab/vre_template_tool

see also https://github.com/inab/openVRE/wiki/Bring-your-own-tool#how-to-bring-in-a-new-tool

on a mac, first install realpath from https://github.com/user454322/realpath

look at the configure-script for configuration:

./configure -b /usr/local/ -m /usr/local/man

TODOs:

• @Laia: Please add the following two data types:
• missing_code_label_table
• consistency_check_table

Requirements

• Install the dependencies used by the Wrapper.

Depends on: R (>=4.0), from CRAN: dataquieR (>=1.0.5), openxlsx (>=4.2.3)

• Install the Wrapper dependencies.

  • Python 3.6 or +
  • Python3.6-dev and Python3.6-venv or +
  • mg-tool-api: https://github.com/Multiscale-Genomics/mg-tool-api.git

• Python 3.6 or later
• git

sudo apt update
sudo apt install python3
sudo apt install git

In order to install the Python dependencies you need pip and venv modules.

sudo apt install python3-pip python3-venv

Installation

cd $HOME

git clone ...

cd dataquierVRE

Create the Python environment

python3 -m venv $HOME/dataquierVRE/venv
source venv/bin/activate
pip install -r requirements.txt

or with relative paths:

python3 -m venv venv
source venv/bin/activate
pip install --upgrade wheel
pip install -r requirements.txt

VRE template Tool Executor

Run the Wrapper

First, go to tests/basic/ to change config.json and in_metadata.json files.

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

License

• University Medicine Greifswald 2021

Licensed under the Apache License, version 2.0 https://www.apache.org/licenses/LICENSE-2.0, see the file LICENSE.txt for details.