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Commit 4c28bf28 authored by selva's avatar selva
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Update working tutorials

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1 merge request!11update Documentation
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docs/source/conf.py
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...@@ -35,10 +35,10 @@ release = "0.0.1" ...@@ -35,10 +35,10 @@ release = "0.0.1"
# Add any Sphinx extension module names here, as strings. They can be # Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones. # ones.
extensions = ["myst_parser", "sphinx.ext.autodoc",'sphinx_tabs.tabs']
napoleon_google_docstring = False napoleon_google_docstring = False
extensions = ["myst_parser", "sphinx.ext.autodoc","sphinx_tabs.tabs","sphinx.ext.napoleon","sphinx.ext.autodoc.typehints"]
napoleosn_use_param=True
# Add any paths that contain templates here, relative to this directory. # Add any paths that contain templates here, relative to this directory.
templates_path = ["_templates"] templates_path = ["_templates"]
...@@ -58,13 +58,13 @@ exclude_patterns = [] ...@@ -58,13 +58,13 @@ exclude_patterns = []
# Add any paths that contain custom static files (such as style sheets) here, # Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files, # relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css". # so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = [] html_static_path = ['_static']
sphinx_tabs_valid_builders = ['linkcheck'] sphinx_tabs_valid_builders = ['linkcheck']
sphinx_tabs_disable_tab_closing = True sphinx_tabs_disable_tab_closing = True
html_css_files=['https://raw.githack.com/ines/termynal/master/termynal.css'] html_css_files=['https://raw.githack.com/Ganz1285/termynal/master/termynal.css']
sphinx_tabs_disable_css_loading = True sphinx_tabs_disable_css_loading = True
......
docs/source/getting_started/Installation.md
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...@@ -23,7 +23,7 @@ To Install **BiTIA** using pip, run this command: ...@@ -23,7 +23,7 @@ To Install **BiTIA** using pip, run this command:
## Configuration ## Configuration files
_TODO_: Order of searching configuration file. _TODO_: Order of searching configuration file.
......
docs/source/getting_started/Working.md
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# Working with BiTIA CLI # WORKING WITH BiTIA
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>
<span data-ty>Usage: python -m bitia [OPTIONS] COMMAND [ARGS]...
<b>Callback</b>
<b><i>Options</i></b> <br><br>
<b>--verbose</b> [debug|info|warning] [default: VerbosityLevel.warning]<br>
<b>--plain</b> --no-plain [default: no-plain]&nbsp;&nbsp;&nbsp;<br>
<b>--server</b> TEXT [default: None] <br>
<b>--install-completion</b> Install completion for the current shell. <br>
<b>--show-completion</b> Show completion for the current shell, to copy it or customize the installation. <br>
<b>--help </b> Show this message and exit. <br>
<b><i>Commands</i></b> <br><br>
<b>checksum</b> value that represents the number of bits in a transmission message<br>
<b>create-container</b> Create container for the pipeline. The container starts running immediately on the server. Use command `logs` to stream the output. <br>
<b>list-container</b> List the remote server associated with the pipeline. <br>
<b>logs</b> Stream logs for the most recent run of a given pipeline. <br>
<b>run</b> Run a pipeline <br>
<b>submit</b> Submit your pipelin (url, directory, zip_file). <br>
<b>version</b> version information <br>
</span>
</div>
The three commands that are the core of BiTIA's functionality are: The three commands that are the core of BiTIA's functionality are:
- run - run
- submit - submit
...@@ -7,11 +38,27 @@ The three commands that are the core of BiTIA's functionality are: ...@@ -7,11 +38,27 @@ The three commands that are the core of BiTIA's functionality are:
<link type="text/css" href="../_static/./css/termynal.css" /> <link type="text/css" href="../_static/./css/termynal.css" />
### Bitia run can be employed in the following ways: ## Bitia run
<div id="termynal1" data-termynal>
<span data-ty="input"><b>python -m bitia run --help</span>
<span data-ty>
Usage: python -m bitia run [OPTIONS] USER_INPUT<br>
Run a pipeline<br>
<b><i>Arguments</i></b> <br><br>
\* <b>user_input</b> TEXT [default: None] [required]<br><br>
<i><b>Options</i></b> <br><br>
<b>--rerun</b> --no-rerun [default: no-rerun]
<b>--output-lines </b> TEXT<
<b>--help </b> Show this message and exit.
</span>
</div>
#### 1. Running commands ### 1. Running commands
<div id="termynal" data-termynal> <div id="termynal2" 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> <span data-ty="progress"></span>
</div> </div>
...@@ -30,9 +77,9 @@ The above code will: ...@@ -30,9 +77,9 @@ The above code will:
- Display the resulting output to the user console - Display the resulting output to the user console
#### 2. Running Pipelines ### 2. Running Pipelines
<div id="termynal1" data-termynal> <div id="termynal3" data-termynal>
<span data-ty="input">bitia run pipeline.sh</span> <span data-ty="input">bitia run pipeline.sh</span>
<span data-ty="progress"></span> <span data-ty="progress"></span>
</div> </div>
...@@ -61,10 +108,10 @@ The above code will: ...@@ -61,10 +108,10 @@ The above code will:
- executing the commands given in the pipeline - executing the commands given in the pipeline
- Displays the resulting output to the user console - Displays the resulting output to the user console
#### 3. Running Directories with multiple required files ### 3. Running Directories with multiple required files
<div id="termynal3" data-termynal> <div id="termynal4" data-termynal>
<span data-ty="input">bitia run work/</span> <span data-ty="input">bitia run work/</span>
<span data-ty="progress"></span> <span data-ty="progress"></span>
</div> </div>
...@@ -106,6 +153,6 @@ The above code will: ...@@ -106,6 +153,6 @@ The above code will:
- Displays the resulting output to the user console - 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> <script type="text/javascript" src="https://raw.githack.com/tiangolo/fastapi/master/docs/en/docs/js/termynal.js" data-termynal-container="#termynal|#termynal1|#termynal2|#termynal3|#termynal4"></script>
docs/source/index.md
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...@@ -62,9 +62,5 @@ If you want to learn how to use BiTIA and installation, check out the following ...@@ -62,9 +62,5 @@ If you want to learn how to use BiTIA and installation, check out the following
- 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)
<!--
```{eval-rst}
.. automodule:: bitia
``` -->
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