diff --git a/docs/source/getting_started/Installation.md b/docs/source/getting_started/Installation.md index 8b2ab4cfd0bdce386d4ccb45a337e734b8f4e4ad..959eac0c795301f9e015856e7052bf2cfc9f9cce 100644 --- a/docs/source/getting_started/Installation.md +++ b/docs/source/getting_started/Installation.md @@ -7,7 +7,7 @@ BiTIA CLI is available on [PyPi] as [BiTIA]. Installing bitia is very simple, you only need to have [python-pip] installed in your system - +<link type="text/css" href="../_static/./css/termynal.css" /> To Install **BiTIA** using pip, run this command: @@ -20,18 +20,19 @@ To Install **BiTIA** using pip, run this command: + ## Configuration TODO: Order of searching configuration file. **_UNIX_** - + <div id="termynal" data-termynal> - <span data-ty="input">./bitia.toml</span> - <span data-ty="input">~/.bitia.toml</span> - <span data-ty="input">$HOME/.config/bitia.toml</span> - <span data-ty="input">/etc/bitia.toml</span> + <span data-ty="input"> ./bitia.toml </span> + <span data-ty="input"> ~/.bitia.toml </span> + <span data-ty="input"> $HOME/.config/bitia.toml </span> + <span data-ty="input"> /etc/bitia.toml </span> </div> **_WINDOWS_** @@ -44,6 +45,9 @@ TODO: Order of searching configuration file. <script src="../_static/./js/termynal.js" data-termynal-container="#termynal"></script> + + + diff --git a/docs/source/getting_started/Working.md b/docs/source/getting_started/Working.md index ac04b198b50583106f081233ec6beb20e82ca325..c0494a5437eed2ee01d83167e5ab19733eb9e164 100644 --- a/docs/source/getting_started/Working.md +++ b/docs/source/getting_started/Working.md @@ -4,17 +4,19 @@ The three commands that are the core of BiTIA's functionality are: - submit - logs +<link type="text/css" href="../_static/./css/termynal.css" /> ### Bitia run can be employed in following ways: #### 1. Running commands -<div class='termynal' data-termynal> +<div id="termynal" data-termynal> + <span data-ty="input">bitia run "samtools convert < foo.fa|http://y.com/foo.fa >"</span> + <span data-ty="progress"></span> +</div> -<span data-ty="input">bitia run "samtools convert <foo.fa|http://y.com/foo.fa>"</span> -</div> The above code will: - Checks for the input file `foo.fa` in the current working directory @@ -30,11 +32,13 @@ The above code will: #### 2. Running Pipelines -<div class='termynal' data-termynal> +<div id="termynal" data-termynal> + <span data-ty="input">bitia run "samtools convert < foo.fa|http://y.com/foo.fa >"</span> + <span data-ty="progress"></span> +</div> + -<span data-ty="input">bitia run pipeline.sh</span> -</div> for `pipeline.sh`: ```bash @@ -56,3 +60,7 @@ The above code will: - Installing the given commands `fastqc`, `trim_galore`,`hisat2` . - executing the commands given in the pipeline - Displays the resulting output to the user console + + + +<script src="../_static/./js/termynal.js" data-termynal-container="#termynal"></script> \ No newline at end of file