Include more working examples

docs/source/getting_started/Installation.md

@@ -32,19 +32,20 @@ Try any one of the following command to search for configuration file
 
 **_UNIX_**
                  
-<div id="termynal1" 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>
-</div>
+> - ./bitia.toml  
+> - ~/.bitia.toml  
+> - $HOME/.config/bitia.toml 
+> - /etc/bitia.tom
+
                   
 **_WINDOWS_**              
                     
- <div id="termynal2" data-termynal>
-    <span data-ty="input"> bitia.toml  </span>
-    <span data-ty="input"> %APPDATA%\bitia.toml  </span>
-    <span data-ty="input"> %PROGRAMDATA%\bitia.toml  </span>
+
+> - bitia.toml
+> - \%APPDATA%\bitia.toml
+> - \%PROGRAMDATA%\bitia.toml
+
+
 </div>                 
 
 

docs/source/getting_started/Working.md

@@ -12,7 +12,7 @@ The three commands that are the core of BiTIA's functionality are:
 #### 1. Running commands
 
 <div id="termynal" data-termynal>
-    <span data-ty="input">bitia run "samtools convert < foo.fa|http://y.com/foo.fa >"</span>
+    <span data-ty="input">bitia run "samtools convert <foo.fa|http://y.com/foo.fa>"</span>
     <span data-ty="progress"></span>
 </div>
 
@@ -61,11 +61,51 @@ The above code will:
     - executing the commands given in the pipeline
 - Displays the resulting output to the user console
 
+#### 3. Running Directories with multiple required files
 
 
+<div id="termynal3" data-termynal>
+    <span data-ty="input">bitia run work/</span>
+    <span data-ty="progress"></span>
+</div>
 
-<script type="text/javascript" src="https://raw.githack.com/tiangolo/fastapi/master/docs/en/docs/js/termynal.js" data-termynal-container="#termynal|#termynal1"></script>
-           
 
+Here `work` directory has two files `main.bitia.sh` and `input_file_links.txt`
+
+for `main.bitia.sh`:
+```bash
+#!/usr/bin/env bash
+
+fastqc *.gz
+
+for file in *_1.fastq.gz
+do
+   trim_galore --cores 8 --gzip --fastqc --max_n 2 --output_dir Trimmed_Data/ --paired $file ${file%_1.fastq.gz}_2.fastq.gz
+done
+
+hisat2-build -p 8 ./Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa index
+```
+
+and `input_file_links.txt`
+```bash
+ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR200/058/SRR20076358/SRR20076358_1.fastq.gz
+ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR200/058/SRR20076358/SRR20076358_2.fastq.gz
+ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR200/061/SRR20076361/SRR20076361_1.fastq.gz
+ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR200/061/SRR20076361/SRR20076361_2.fastq.gz
+ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR200/063/SRR20076363/SRR20076363_1.fastq.gz
+ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR200/063/SRR20076363/SRR20076363_2.fastq.gz
+```
+
+
+The above code will:
+- Extract the given directory with `main.bitia.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 by:
+    - Downloading the given input files which are mentioned in `input_files.txt`.
+    - Installing the given commands `fastqc`, `trim_galore`,`hisat2`.
+    - Executing the commands given in the pipeline
+- Displays the resulting output to the user console
+
+
+<script type="text/javascript" src="https://raw.githack.com/tiangolo/fastapi/master/docs/en/docs/js/termynal.js" data-termynal-container="#termynal|#termynal1|#termynal3"></script>
+           
 
-                 
\ No newline at end of file