Initial commit

Author: gemygk

.bumpversion.cfg

@@ -0,0 +1,8 @@
+[bumpversion]
+current_version = 0.1.0
+commit = False
+tag = False
+
+[bumpversion:file:pyproject.toml]
+
+[bumpversion:file:README.md]

.gitignore

@@ -172,3 +172,7 @@ cython_debug/
 
 # PyPI configuration file
 .pypirc
+
+# Mac OS
+.DS_Store
+

README.md

@@ -1,2 +1,71 @@
-# vizgen_data_transfer
-Vizgen Data Transfer
+# Vizgen Data Transfer
+
+This repository contains tools and scripts for managing data transfer processes related to Vizgen projects. It is designed to streamline and automate the movement of data between systems.
+
+
+## Prerequisites
+
+- Python 3.11 or higher
+- Required Python packages listed in `pyproject.toml`
+
+## Installation
+
+1. Clone the repository:
+    ```bash
+    git clone https://github.com/EI-CoreBioinformatics/vizgen_data_transfer.git
+    cd vizgen_data_transfer
+    ```
+2. Build and Install using [Poetry](https://python-poetry.org/docs/#installation):
+    ```bash
+    version=0.1.0
+    poetry build
+    pip install --prefix=/path/to/vizgen_data_transfer/${version}/x86_64 -U dist/*whl
+    ```
+3. Set up the environment:
+    ```bash
+    export PATH=/path/to/vizgen_data_transfer/${version}/x86_64/bin:$PATH
+    export PYTHONPATH=/path/to/vizgen_data_transfer/${version}/x86_64/lib/python3*/site-packages:$PYTHONPATH
+    ```
+4. Run the script:
+    ```bash
+    vizgen_data_transfer --help
+    usage: vizgen_data_transfer [-h] [--copy_type COPY_TYPE [COPY_TYPE ...]] [--threads THREADS] [--disk] [--vizgen_config VIZGEN_CONFIG] [--debug] run_id
+
+            Script for Vizgen data transfer
+
+
+    positional arguments:
+    run_id                Provide run name, for example: 202310261058_VZGEN1_VMSC10202
+
+    options:
+    -h, --help            show this help message and exit
+    --copy_type COPY_TYPE [COPY_TYPE ...]
+                            Provide copy type, for example: raw_data, analysis, output (default: ['raw_data', 'analysis', 'output'])
+    --threads THREADS     Number of threads to use for copying (default: 8)
+    --disk                Enable this option if run has to be copied from the Windows external Hard disk 'G:\Vizgen data Z drive' instead of the default Z: Drive on the analysis machine [default:False]
+    --vizgen_config VIZGEN_CONFIG
+                            Path to vizgen config file [default:/path/to/vizgen_data_transfer/dev/x86_64/lib/python3*/site-packages/vizgen_data_transfer/etc/.vizgen_config.toml]
+    --debug               Enable this option for debugging [default:False]
+
+    Contact: Gemy George Kaithakottil (Gemy.Kaithakottil@earlham.ac.uk)
+    ```
+
+## Usage
+
+1. Configure the settings in `.vizgen_config.toml`.
+2. Run the main script:
+    ```bash
+    vizgen_data_transfer --vizgen_config /path/to/.vizgen_config.toml 202310261058_VZGEN1_VMSC10202
+    ```
+
+## Contributing
+
+Contributions are welcome! Please fork the repository and submit a pull request.
+
+## License
+
+This project is licensed under the GNU General Public License. See the `LICENSE` file for details.
+
+## Contact
+
+For questions or support, please contact [Gemy.Kaithakottil@earlham.ac.uk] or [gemygk@gmail.com].

pyproject.toml

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+[project]
+name = "vizgen_data_transfer"
+version = "0.1.0"
+description = "Vizgen Data Transfer"
+authors = [
+    {name = "Gemy George Kaithakottil", email = "Gemy.Kaithakottil@earlham.ac.uk"}
+]
+readme = "README.md"
+requires-python = ">=3.11,<4.0"
+license = {text = "GNU General Public License v3.0"}
+keywords = [
+    "vizgen",
+    "data transfer",
+    "data management",
+    "bioinformatics",
+]
+dependencies = [
+]
+
+[tool.poetry]
+packages = [{include = "vizgen_data_transfer", from = "src"}]
+package-mode = true
+
+[tool.poetry.scripts]
+vizgen_data_transfer = "vizgen_data_transfer.__main__:main"
+
+[build-system]
+requires = ["poetry-core>=2.0.0,<3.0.0"]
+build-backend = "poetry.core.masonry.api"