From 3072db8d5f026c052414004b87256aeb96447669 Mon Sep 17 00:00:00 2001
From: selva <selvaganz1285@gmail.com>
Date: Thu, 20 Oct 2022 10:21:12 +0530
Subject: [PATCH] UPdate termynal
---
docs/source/getting_started/Installation.md | 16 ++++++++++------
docs/source/getting_started/Working.md | 20 ++++++++++++++------
2 files changed, 24 insertions(+), 12 deletions(-)
diff --git a/docs/source/getting_started/Installation.md b/docs/source/getting_started/Installation.md
index 8b2ab4c..959eac0 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 ac04b19..c0494a5 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
--
GitLab