diff --git a/docs/source/conf.py b/docs/source/conf.py index 4bd26318e9f760bc4b3125b81cf3cd5e6e35cac5..f487bb53100744c92c593fbc42b5ac030d0ab2aa 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -58,7 +58,7 @@ exclude_patterns = [] # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ["_static"] +html_static_path = [] sphinx_tabs_valid_builders = ['linkcheck'] diff --git a/docs/source/index.md b/docs/source/index.md index 4185f31931c361e10c29c1075509b908563d1234..a0f599f5e16563b88bbd3eac04a860ce2346adc0 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -16,7 +16,7 @@ Welcomme to BiTIA Documentation! -BiTIA is a tool that simplifies the infrastructure required to run complex bioinformatics pipelines. BiTIA plays well with the existing pipeline solution such as snakemake. +BiTIA is a tool that simplifies the infrastructure required to run complex bioinformatics pipelines. BiTIA plays well with the existing workflow managements systems such as [snakemake](https://snakemake.readthedocs.io/en/stable/), [gnu-Make](https://www.gnu.org/software/make/), etc. BiTIA has two components: **bitia-cli** and **bitia-runner**. BiTIA CLI is on the clientside and allows clients to submit tasks to the bitia server. @@ -40,71 +40,17 @@ getting_started/Working If you want to learn how to use BiTIA and installation, check out the following resources: -<details > -<summary><b>REQUIREMENTS</b></summary> - -> - Python 3.8+ -</details> -<details> -<summary><b>INSTALLATION & CONFIGURATION</b></summary> - - To Install BiTIA using pip, run this command: - ```{eval-rst} - .. tabs:: - - .. group-tab:: Unix - - .. code-block:: bash - - $ python3 -m pip install bitia - - - .. group-tab:: Windows - - .. code-block:: bash - - $ python3 -m pip install bitia - ``` - -**Configuration** - - -TODO: Order of searching configuration file. - - - ```{eval-rst} - .. tabs:: - - .. group-tab:: Unix - - .. code-block:: bash - - 1. ./bitia.toml - 2. ~/.bitia.toml - 3. $HOME/.config/bitia.toml - 4. /etc/bitia.toml - - .. group-tab:: Windows - - .. code-block:: bash - - 1. bitia.toml - 2. %APPDATA%\bitia.toml - 3. %PROGRAMDATA%\bitia.toml - ``` -</details> - -<details> -<summary><b>GETTING_STARTED</b></summary> +### **GETTING_STARTED** - To Learn about Bio-Informatics pipelines ofs RNA-seq analysis refer [Bioinformatics pipelines](https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/) -- To Understand working with BiTIA refer [Working with BiTIA CLI](getting_started/Working.md) - -</details> +- **REQUIREMENTS** + - Python 3.8+ +- [**INSTALLATION & CONFIGURATION**](getting_started/Installation.md) +- To Understand working with BiTIA refer [Working with BiTIA CLI](getting_started/Working.md) <!--