# Execution

## Execution in command line

### Binary path configuration

First off, we recommend to configure binary paths in your environment in order to ease the command line execution. For doing that, please follow the next steps:

#### Create binary folder

Remember to change the */home/user_name/projects/* path to the real path on your computer.

```Shell
mkdir /home/user_name/projects/bin
```

#### Change python file permissions

Remember to change the */home/user_name/projects/* path to the real path on your computer.

```Shell
chmod +x /home/user_name/projects/biobb_template/biobb_template/template/template.py
```

#### Create symlink to python file

Remember to change the */home/user_name/projects/* path to the real path on your computer.

```Shell
cd /home/user_name/projects/bin
ln -s /home/user_name/projects/biobb_template/biobb_template/template/template.py template
```

#### Create conda activate actions

Remember to change the */[anaconda-path]* and the */home/user_name/projects/* path to the real paths on your computer.

```Shell
cd /[anaconda-path]/envs/biobb_template/etc
mkdir conda
cd conda/
mkdir activate.d
cd activate.d/
printf '#!/usr/bin/env bash\n\nexport BIOBB_OLD_PATH=$PATH\nexport PATH=/home/user_name/projects/bin:$PATH\n' > biobb_template.sh
```

#### Create conda deactivate actions

Remember to change the */[anaconda-path]* and the */home/user_name/projects/* path to the real paths on your computer.

```Shell
cd /[anaconda-path]/envs/biobb_template/etc/conda
mkdir deactivate.d
cd deactivate.d/
printf '#!/usr/bin/env bash\n\nexport PATH=$BIOBB_OLD_PATH\n' > biobb_template.sh
```

#### Restart environment

```Shell
conda deactivate
conda activate biobb_template
```

### Execution

All the information about the command line execution of a **BioBB** can be found here:

[https://biobb-template.readthedocs.io/en/latest/command_line.html](https://biobb-template.readthedocs.io/en/latest/command_line.html)

## Execution in Jupyter Notebook

**Jupyter Notebook** (formerly IPython Notebooks) is a web-based interactive computational environment for creating [Jupyter](https://jupyter.org/) notebook documents. The *notebook* term can colloquially make reference to many different entities, mainly the Jupyter web application, Jupyter Python web server, or Jupyter document format depending on context. A **Jupyter Notebook** document is a JSON document, following a versioned schema, and containing an ordered list of **input/output cells** which can contain code, text (using Markdown), mathematics, plots and rich media, usually ending with the ".ipynb" extension.

A Jupyter Notebook can be converted to a number of open standard output formats (**HTML**, **presentation slides**, **LaTeX**, **PDF**, **ReStructuredText**, **Markdown**, **Python**) through *Download As* in the web interface, via the nbconvert library or *jupyter nbconvert* command line interface in a shell.

To simplify visualisation of **Jupyter Notebook** documents on the web, the nbconvert library is provided as a service through NbViewer which can take a URL to any publicly available notebook document, convert it to **HTML on the fly** and display it to the user.

Basic examples of **Jupyter Notebook** execution for *biobb_template* can be found here:

[https://github.com/bioexcel/biobb_template/blob/master/biobb_template/notebooks/template/template.ipynb](https://github.com/bioexcel/biobb_template/blob/master/biobb_template/notebooks/template/template.ipynb)

The execution is pretty straightforward: 

1. We must **create an object** with the tool **properties** in case the properties are mandatory for this tool. More information about the properties [clicking here](https://biobb-documentation.readthedocs.io/en/latest/arguments.html#properties).

2. We call the **tool class** with the mandatory **inputs** / **outputs** and the **properties** defined in the previous step.


```python
prop = {
    "boolean_property": False,
    "remove_tmp": True
}
template(input_file_path1=input1, 
         input_file_path2=input2, 
         output_file_path=output, 
         properties=prop)
```

After executing this cell in **Jupyter Notebook** we will get the output log generated by the tool. In the example above, it should be something like this:


```python
2020-02-20 17:34:14,566 [MainThread  ] [INFO ]  Creating 19838984-a76c-401e-9226-4a814268391c temporary folder
2020-02-20 17:34:14,587 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments
2020-02-20 17:34:14,597 [MainThread  ] [INFO ]  Appending optional argument to command line
2020-02-20 17:34:15,173 [MainThread  ] [INFO ]  zip -j output 19838984-a76c-401e-9226-4a814268391c/input1 19838984-a76c-401e-9226-4a814268391c/input2

2020-02-20 17:34:15,178 [MainThread  ] [INFO ]  Exit code 0

2020-02-20 17:34:15,181 [MainThread  ] [INFO ]    adding: input1 (deflated 87%)
  adding: input2 (deflated 14%)

2020-02-20 17:34:15,191 [MainThread  ] [INFO ]  Removed: 19838984-a76c-401e-9226-4a814268391c
```

## Execution in a workflow

TODO