# Run the pipeline


## Initialize your project

1. Open a terminal
2. Activate your environment `conda activate ipasuite`
3. Generate your project folder `ipasuite init [project]`

A project folder will be created with all the necessary files for workflow execution
You can access this folder by a file browser or doing `cd [name of your project]`


## Configure your project

4. Configure your pipeline using the [configurator](configuration)  `cd [name of your project]; ipasuite config` 
5. Fill up your experiments in `samples.tsv` specifing where to find your raw data ([See configuration](configuration))
   and QuShape projects if you already treated some experiments

## Run pipeline

6. Run `ipasuite qushape` it will run the first part of the workflow and open QuShape
   for each file to treat. You must follow every step of QuShape
   and save the QuShape file. You can follow the [QuShape Tutorial of the Weeks
   lab](QuShape_Tutorial.pdf) or the version of the Sargueil lab.
7. Run `ipasuite run`

`ipasuite` will generate structure models in results/5.3-structure and results/5.4-varna treated
with ipanemap as set up in your configuration file

## In case of trouble :

Two commands can help debugging :

```bash
ipasuite check
```
Will check :
- If some input files are missing
- If all necessary samples are available to run IPANEMAP and the footprint analysis
- If samples are duplicated
- If some raw files are identical

```bash
ipasuite log
```
Will show pipeline scripts log

## Clean file

at any point, you can clean pipeline files :

```bash
ipasuite clean
```

It will remove by default all files, figures and logs downstream
qushape treatement. You can choose from which step to remove
file using `--from-step`

To only clean log files:
```bash
ipasuite log --clean
```