diff --git a/docs/source/getting_started.md b/docs/source/getting_started.md index 7b896a44a3beff961d91e9ecde71dc272f30509d..e767161ca076d407e086b52bd521fca319bd2f6d 100644 --- a/docs/source/getting_started.md +++ b/docs/source/getting_started.md @@ -1,14 +1,15 @@ # Getting Started +BiTIA CLI is the Command Interface tool helpful in getting user inputs with commands and required files, directories etc. -## Installation -BiTIA is available on PyPi. +This submits jobs to the server, which contains bitia-runner that works on the job and produce results -To get started with using BiTIA, you should [install Python] and make sure [python-pip] is installed with it on your system. +**To work with BiTIA, we need to install bitia-cli and submit jobs to the server** +## Installing bitia +Installing bitia is very simple, you only need to have [python-pip] installed in your system -[install Python]: https://realpython.com/installing-python/ -[python-pip]: https://pypi.org/project/pip/ -### Ensure you have a working pip +BiTIA CLI is available on [PyPi] as [BiTIA]. +#### Ensure you have a working pip As a first step, you should check that you have a working Python with pip installed. This can be done by running the following commands and making @@ -26,7 +27,12 @@ If that worked, congratulations! You have a working pip in your environment. To Install **BiTIA** using pip: -```bash +``` $ python3 -m pip install bitia ``` + +[BiTIA]: https://pypi.org/project/bitia/ +[Pypi]: https://pypi.org/ +[install Python]: https://realpython.com/installing-python/ +[python-pip]: https://pypi.org/project/pip/ \ No newline at end of file diff --git a/docs/source/index.md b/docs/source/index.md index d23f29fd991a6bdc7a33b436a96497b5158d67a2..5abd1b3fceb7db1c2bd6851e85454ce8bac97320 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -1,16 +1,24 @@ ## BioInformatics Tool for Infrastructure Automation (BiTIA) + ```{image} https://img.shields.io/pypi/v/bitia.svg :target: https://pypi.python.org/pypi/bitia ``` ```{image} https://img.shields.io/pypi/pyversions/bitia.svg :target: https://www.python.org ``` +BiTIA is a tool that simplifies the infrastructure required to run complex bioinformatics pipelines. BiTIA plays well with the existing pipeline solution such as snakement. - -BiTIA makes it easy to orchestrate the infrastructure required to run -complex bioinformatics pipelines. BiTIA plays well with existing pipeline -solution such as snakemake. [See some examples] +BiTIA has two components: bitia-cli and bitia-runner. +- **bitia-cli** +Creates a zip file of the user input(pipeline) containing a unique hash and ships it to the server. +- **bitia-runner** + Runs following works in the server + - Creates a docker container with the user input + - Runs the pipeline + - Sends log to the user + - Sends link of results(artifacts) to the user + - Interacts with common cache for reading data/reference files [see some examples]: examples @@ -18,7 +26,6 @@ solution such as snakemake. [See some examples] ```{toctree} :caption: Getting started :hidden: true -:maxdepth: 1 :name: getting_started getting_started @@ -26,7 +33,7 @@ developer ``` -If you want to learn how to use BiTIA, check out the following resources: +If you want to learn how to use BiTIA and installation, check out the following resources: - [Getting Started](getting_started.md)