==========
SubmitCGAP
==========
A file submission tool for CGAP
===============================
.. image:: https://travis-ci.org/dbmi-bgm/SubmitCGAP.svg
:target: https://travis-ci.org/dbmi-bgm/SubmitCGAP
:alt: Build Status
.. image:: https://coveralls.io/repos/github/dbmi-bgm/SubmitCGAP/badge.svg
:target: https://coveralls.io/github/dbmi-bgm/SubmitCGAP
:alt: Coverage
.. image:: https://readthedocs.org/projects/submitcgap/badge/?version=latest
:target: https://submitcgap.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
Description
===========
This is a tool for uploading certain kinds of files to CGAP.
Current support is for submission of new cases, family histories, and gene lists.
Installation
============
Installing this system involves these steps:
1. Create, install, and activate a virtual environment.
2. *Only if you are a developer*, install poetry and select the source repository.
Others will not have a source repository to select,
so should skip this step.
3. If you are an end user, do "``pip install submit_cgap``".
Otherwise, do "``make build``".
4. Set up a ``~/.cgap-keys.json`` credentials file.
For detailed information about these installation steps, see
`Installing SubmitCGAP <https://submitcgap.readthedocs.io/en/latest/installation.html>`_.
Testing
=======
To run unit tests, do::
$ make test
Additional notes on testing these scripts for release can be found in
`Testing SubmitCGAP <TESTING.rst>`__.
Getting Started
===============
Once you have finished installing this library into your virtual environment,
you should have access to the ``submit-metadata-bundle`` and the ``submit-genelist``
commands. For more information about how to format files for submission and how to
use these commands, see `Getting Started <https://submitcgap.readthedocs.io/en/latest/usage.html>`_.
Raw data
{
"_id": null,
"home_page": "https://github.com/dbmi-bgm/SubmitCGAP",
"name": "submit_cgap",
"maintainer": null,
"docs_url": null,
"requires_python": "<3.13,>=3.8.1",
"maintainer_email": null,
"keywords": "submit cgap, submitcgap",
"author": "4DN-DCIC Team",
"author_email": "support@4dnucleome.org",
"download_url": "https://files.pythonhosted.org/packages/98/9f/6f9071bb17ca254f47b79bdd2a8ac39bf7deac1d34fbbfd0ec8c8973ff44/submit_cgap-4.2.0.tar.gz",
"platform": null,
"description": "==========\nSubmitCGAP\n==========\n\n\nA file submission tool for CGAP\n===============================\n\n.. image:: https://travis-ci.org/dbmi-bgm/SubmitCGAP.svg\n :target: https://travis-ci.org/dbmi-bgm/SubmitCGAP\n :alt: Build Status\n\n.. image:: https://coveralls.io/repos/github/dbmi-bgm/SubmitCGAP/badge.svg\n :target: https://coveralls.io/github/dbmi-bgm/SubmitCGAP\n :alt: Coverage\n\n.. image:: https://readthedocs.org/projects/submitcgap/badge/?version=latest\n :target: https://submitcgap.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\nDescription\n===========\n\nThis is a tool for uploading certain kinds of files to CGAP.\n\nCurrent support is for submission of new cases, family histories, and gene lists.\n\n\nInstallation\n============\n\nInstalling this system involves these steps:\n\n1. Create, install, and activate a virtual environment.\n2. *Only if you are a developer*, install poetry and select the source repository.\n Others will not have a source repository to select,\n so should skip this step.\n3. If you are an end user, do \"``pip install submit_cgap``\".\n Otherwise, do \"``make build``\".\n4. Set up a ``~/.cgap-keys.json`` credentials file.\n\nFor detailed information about these installation steps, see\n`Installing SubmitCGAP <https://submitcgap.readthedocs.io/en/latest/installation.html>`_.\n\n\nTesting\n=======\n\nTo run unit tests, do::\n\n $ make test\n\nAdditional notes on testing these scripts for release can be found in\n`Testing SubmitCGAP <TESTING.rst>`__.\n\n\nGetting Started\n===============\n\nOnce you have finished installing this library into your virtual environment,\nyou should have access to the ``submit-metadata-bundle`` and the ``submit-genelist``\ncommands. For more information about how to format files for submission and how to\nuse these commands, see `Getting Started <https://submitcgap.readthedocs.io/en/latest/usage.html>`_.\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "Support for uploading file submissions to the Clinical Genomics Analysis Platform (CGAP).",
"version": "4.2.0",
"project_urls": {
"Homepage": "https://github.com/dbmi-bgm/SubmitCGAP",
"Repository": "https://github.com/dbmi-bgm/SubmitCGAP.git"
},
"split_keywords": [
"submit cgap",
" submitcgap"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "9ecffacf0623793f026ec013e45b5584b1c79e8b5eb451a6839c6d0a47186a57",
"md5": "8cca369476fcd7a8558c48122f305a2c",
"sha256": "740bea9a44e299cf4ce3f8988f97c0dfc73d75720ab8441a11645465d0a208a3"
},
"downloads": -1,
"filename": "submit_cgap-4.2.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "8cca369476fcd7a8558c48122f305a2c",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": "<3.13,>=3.8.1",
"size": 109548,
"upload_time": "2024-07-03T16:16:02",
"upload_time_iso_8601": "2024-07-03T16:16:02.261501Z",
"url": "https://files.pythonhosted.org/packages/9e/cf/facf0623793f026ec013e45b5584b1c79e8b5eb451a6839c6d0a47186a57/submit_cgap-4.2.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "989f6f9071bb17ca254f47b79bdd2a8ac39bf7deac1d34fbbfd0ec8c8973ff44",
"md5": "edfc7a0e3a55ce35b2205f78d4abd5e4",
"sha256": "76d1cfbd3b88f4fad322d55a371499ebbf9e7cd98a4cff07fcc3e6c0c35ddb17"
},
"downloads": -1,
"filename": "submit_cgap-4.2.0.tar.gz",
"has_sig": false,
"md5_digest": "edfc7a0e3a55ce35b2205f78d4abd5e4",
"packagetype": "sdist",
"python_version": "source",
"requires_python": "<3.13,>=3.8.1",
"size": 81003,
"upload_time": "2024-07-03T16:16:04",
"upload_time_iso_8601": "2024-07-03T16:16:04.311012Z",
"url": "https://files.pythonhosted.org/packages/98/9f/6f9071bb17ca254f47b79bdd2a8ac39bf7deac1d34fbbfd0ec8c8973ff44/submit_cgap-4.2.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-07-03 16:16:04",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "dbmi-bgm",
"github_project": "SubmitCGAP",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "submit_cgap"
}
JSON
