diff --git a/docs/source/getting_started/Installation.md b/docs/source/getting_started/Installation.md index 45c548e98e67e3cfd0850174a6ecfd1317c0d18a..e1b4a2602f345b6aaa14994fc95e15c3f223fc67 100644 --- a/docs/source/getting_started/Installation.md +++ b/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> diff --git a/docs/source/getting_started/Working.md b/docs/source/getting_started/Working.md index e550e189e1324494b0cf2c7b5beee8bc304c532e..610e2527dd44e9651079e8757ac0a38d0a29ad87 100644 --- a/docs/source/getting_started/Working.md +++ b/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 diff --git a/docs/source/img/BiTIA_New_Age.jpg b/docs/source/img/BiTIA_New_Age.jpg deleted file mode 100644 index 5d3f22c316856d1feae44d4b180f732eb4e5f8e1..0000000000000000000000000000000000000000 Binary files a/docs/source/img/BiTIA_New_Age.jpg and /dev/null differ