From 55c8c6ff5fee6f1a8ffc0a10d27dc11b08fc4726 Mon Sep 17 00:00:00 2001
From: selva <selvaganz1285@gmail.com>
Date: Fri, 7 Oct 2022 12:13:46 +0530
Subject: [PATCH] updated documentation
---
docs/source/getting_started.md | 20 +++++++++++++-------
docs/source/index.md | 19 +++++++++++++------
2 files changed, 26 insertions(+), 13 deletions(-)
diff --git a/docs/source/getting_started.md b/docs/source/getting_started.md
index 7b896a4..e767161 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 d23f29f..5abd1b3 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)
--
GitLab