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Commit 2cb3c92c authored by selva's avatar selva
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changes of typos

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# 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`
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<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**
&nbsp; For executing any single task of BioInformatics pipeline, we can instruct Bitia specific single-line commands.
&nbsp; For executing any single task of bioInformatics pipeline, we can instruct Bitia specific single-line commands.
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......@@ -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
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