# Configuration 

To run the pipeline on your project, you must fill in 2 configuration files

- `config.yaml` Which contains general configuration
- `samples.tsv` That contains informations about samples and replicates


## 1. Fill in `config.yaml`  using `ipasuite config`

Once you generated your project using `ipasuite init [project]` and enter your project using `cd [project]`

Launch `ipasuite config`. Fill in the form into your webbrowser and save.

For detailed information see ![Advanced configuration](config_yaml_ref.md)

![An illustration of the configurator web interface](configurator.png)




<!-- 
In order to get started with your project, you might look at thoses sections of
`config.yaml` or in the local web configurator:

sequences
: List the RNA molecules used in this project, and the path to there sequence

conditions
: List the experimental conditions which will be explored in this project

format
: Choose how the files will be named, in relation the your `conditions` section

rawdata
: If you want to import files from previous analysis, you should modify this section

qushape
: Input the configuration used with your capillary sequencer. (Channels) 

ipanemap
: Configure the execution conditions for IPANEMAP

footprint
: Configure the excutions of diffential analysisk

Others sections can stay untouch depending of your needs

To go futher : [](config_yaml_ref)
-->

## 2. Fill in `samples.tsv`

1. Open your project folder using a file browser
2. Open samples.tsv in libreoffice calc.
3. Create conditions columns and comments columns

For each condition declared in `ipasuite config` you must create a column with the same
identifier in samples.tsv

In addition, you can add arbitrary other columns to your file `samples.tsv`. These additional columns can contain useful annotations and comments that help to classify and characterize your data, but are otherwise ignored by the IPANEMAP Suite. Each column must have a unique name.

3. Create a row for each of your experiments:
For each experiment, you must create a corresponding row, and fill in the following
informations

    id (string)
    : a unique number as experiment identifier
    
    rna_id (string)
    : The identifier for RNA fragment used in this experiment, as declared in the `sequences` section of `ipasuite config`
    
    ddNTP (ddA, ddT, ddG, ddC)
    : Indicate the ddNTP used for the sequencing condition of capillary eletrophoresis
    
    date (date)
    : Date of the experiment. use YYYY-MM-DD 
    
    replicate (integer)
    : id for the experiment and the given probing condition
      this identifier, allows distinguishing the different replicates for a given condition. Must be unique for a given condition.

If you activated «subsequence» in `ipasuite config`, you must also fill in `rt_begin_pos` and `rt_end_pos`:

    rt_begin_pos (integer)
    : Position of the first nucleotide after reverse transcriptase primer used for this
    sample

    rt_end_pos (integer)
    : Position of the last nucleotide reachable by the reverse transcriptase (which is
    most of the time 0)

Since Reverse transcription occurs from 3' to 5' `rt_begin_pos > rt_end_pos`


You must fill in every condition column declared in `ipasuite config`.


(A missing value in one of the mandatory or condition columns will cause an error when launching `ipasuite run`)

4. Fill in file information

For each row, you must give information about where to find raw data :

probe_file (relative file path)
: relative path to the sequencing file corresponding to this shape sample. 

control_file (relative file path)
: relative path to the file sequencing file corresponding to the control (DMSO) file of this shape sample.

reference_qushape_file (file path) (optional)
: If using Reference QuShape project : will be used in QuShape to pre-generate peak calling and alignment

qushape_file (optional)
: Direct import of QuShape projects : Filling this field let you to import readily treated QuShape data. If this field specifies a file, IPANEMAP Suite will try to import it as QuShape file, unless there is already a corresponding file in `results/2-qushape`. If a QuShape file is specified, `probe_file` and `control_file` are ignored.
The file can be specified with a path relative to the path prefix as
specified in the configuration of the project.

reference_qushape_file
: Specify a reference file for QuShape. Use this to specify a template for QuShape.

map_file
: Direct import of map files : This field let you to import normalized reactivity data from other sources (e.g. ShapeMapper2) as map files. If a file is specified, IPANEMAP Suite imports it and ignores all other specifications of data for the experiment.
The file can be specified with a path relative to the path prefix as
specified in the configuration of the project.

discard
: This columns allows you to mark experiment data rows that should be ignored by IPANEMAP Suite. This can help to keep a record of disregarded data in `samples.tsv` or temporarily take out data.

<!--
For each type of experimental condition, you must declare it in the `condition_names` of `config.yaml` file the name declared in the config file must be the same as the on in `samples.tsv`
In order to generate unambiguous file name, you must also add the conditions in the `format` section



#### Examples :

probe (string)
: Which probe was used in this sample (1M7, BzCN, NMIA, DMS, etc.)

temperature (int)
: temperature At which probing was
performed 

magnesium (string)
: Did the sample buffer contained Magnesium during probing (Mg / noMg)?

interaction (string)
: What other molecule/RNA was present with the probed RNA during the probing step.

### Optional columns
-->