diff --git a/docs/source/getting_started/Working.md b/docs/source/getting_started/Working.md index eb06fceb21a79ce687e337fa3ba2d21465f1b5d4..224c06e391fa2142f0ae49384fddbd1d95f47993 100644 --- a/docs/source/getting_started/Working.md +++ b/docs/source/getting_started/Working.md @@ -1,6 +1,6 @@ # WORKING WITH BiTIA -To List available commands and options in bitia, execute `bitia --help` +To list available commands and options in bitia, execute `bitia --help` <div id="termynal" data-termynal> <span data-ty="input">python -m bitia --help </span> @@ -58,13 +58,13 @@ Usage: python -m bitia run [OPTIONS] USER_INPUT<br> The Argument `user_input` can be used in three ways: -1. Executing Commands +1. Executing commands 2. Executing pipelines -3. Executing Directories with multiple required files +3. Executing directories with multiple required files **1. Executing Commands** - For executing any single task of BioInformatics pipeline, we can instruct Bitia specific single-line commands. + For executing any single task of bioInformatics pipeline, we can instruct Bitia specific single-line commands. <div id="termynal2" data-termynal> @@ -76,12 +76,12 @@ The Argument `user_input` can be used in three ways: The above code will: - Checks for the input file `foo.fa` in the current working directory -- 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. +- Download the input file from `http://example.com/foo.fa` and name it `foo.fa` +- Add the 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 from the link `http://example.com/foo.fa` and name it `foo.fa` + - Downloading the given input file from `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