From 53f4d2b575581edfc727d346735389dd4da744e8 Mon Sep 17 00:00:00 2001
From: selva <selvaganz1285@gmail.com>
Date: Thu, 20 Oct 2022 12:30:55 +0530
Subject: [PATCH] Edit typos
---
docs/source/getting_started/Installation.md | 4 ++--
docs/source/getting_started/Working.md | 14 +++++++-------
docs/source/index.md | 12 ++++++------
3 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/docs/source/getting_started/Installation.md b/docs/source/getting_started/Installation.md
index 40f7e0d..22f7f15 100644
--- a/docs/source/getting_started/Installation.md
+++ b/docs/source/getting_started/Installation.md
@@ -1,9 +1,9 @@
<link rel="stylesheet" type="text/css" href="./../_static/./css/termynal.css" />
# BiTIA Installation
-BiTIA CLI is the Command Line Interface Tool which helps in getting user inputs with commands, directories and required files. It sends tasks to the server, where bitia-runner processes them and generates results.
+BiTIA CLI is the Command Line Interface Tool that helps get user inputs with commands, directories, and required files. It sends tasks to the server, where bitia-runner processes them and generates results.
-**To work with BiTIA, we need to install bitia-cli and submit tasks to the server**
+**To work with BiTIA, we need to install bitia-cli and submit tasks to the server**.
## Installing bitia
BiTIA CLI is available on [PyPi] as [BiTIA].
diff --git a/docs/source/getting_started/Working.md b/docs/source/getting_started/Working.md
index c0494a5..143ef77 100644
--- a/docs/source/getting_started/Working.md
+++ b/docs/source/getting_started/Working.md
@@ -7,7 +7,7 @@ The three commands that are the core of BiTIA's functionality are:
<link type="text/css" href="../_static/./css/termynal.css" />
-### Bitia run can be employed in following ways:
+### Bitia run can be employed in the following ways:
#### 1. Running commands
@@ -20,13 +20,13 @@ The three commands that are the core of BiTIA's functionality are:
The above code will:
- Checks for the input file `foo.fa` in the current working directory
-- Download the input file from given link `http://example.com/foo.fa` and name it as `foo.fa`
+- Download the input file from the given link `http://example.com/foo.fa` and name it `foo.fa`
- Add the given command `samtools convert <foo.fa|http://example.com/foo.fa` into a pipeline file.
- Extract the current working directory with the pipeline as a zip file that contains a unique hash and send it to the server `public.bitia.link`
- The BiTIA runner in the server will execute the pipeline by:
- Installing the given command `samtools`
- - Downloading the given input file form the link `http://example.com/foo.fa` and name it as `foo.fa`
- - executing the command `samtools convert foo.fa`
+ - Downloading the given input file from the link `http://example.com/foo.fa` and name it `foo.fa`
+ - Executing the command `samtools convert foo.fa`
- Display the resulting output to the user console
@@ -55,9 +55,9 @@ hisat2-build -p 8 ./Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa i
```
The above code will:
-- Extract the current working directory with the `pipeline.sh` as a zip file that contains a unique hash and sent it to the server `public.bitia.link`
-- The BiTIA runner in the server will execute the pipeline
- - Installing the given commands `fastqc`, `trim_galore`,`hisat2` .
+- Extract the current working directory with the `pipeline.sh` as a zip file containing a unique hash and send it to the public `server.bitia.link`
+- The BiTIA runner in the server will execute the pipeline .
+ - Installing the given commands `fastqc`, `trim_galore`,`hisat2`.
- executing the commands given in the pipeline
- Displays the resulting output to the user console
diff --git a/docs/source/index.md b/docs/source/index.md
index 4d1d9d1..26b604e 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -22,13 +22,13 @@
```
</p>
-Welcomme to BiTIA Documentation!
+Welcome to BiTIA Documentation!
-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 is a tool that simplifies the infrastructure required to run complex bioinformatics pipelines. BiTIA plays well with the existing workflow management 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.
-BiTIA runner is on the serverside and operates the given tasks to produce results.
+BiTIA CLI is on the client side and allows clients to submit tasks to the bitia server.
+BiTIA runner is on the server side and operates the given tasks to produce results.
## **bitia-cli**
Most users only need the `bitia-cli` tool to submit tasks.
@@ -51,7 +51,7 @@ If you want to learn how to use BiTIA and installation, check out the following
### **GETTING STARTED**
-- To Learn about Bio-Informatics pipelines ofs RNA-seq analysis refer
+- To Learn about Bio-Informatics pipelines of RNA-seq analysis, refer
[Bioinformatics pipelines](https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/)
@@ -59,7 +59,7 @@ If you want to learn how to use BiTIA and installation, check out the following
- Python 3.8+
- [**INSTALLATION & CONFIGURATION**](getting_started/Installation.md)
-- To Understand working with BiTIA refer [Working with BiTIA CLI](getting_started/Working.md)
+- To Understand working with BiTIA, refer [Working with BiTIA CLI](getting_started/Working.md)
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