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

  1. Configure your pipeline using the configurator cd [name of your project]; ipasuite config

  2. Fill up your experiments in samples.tsv specifing where to find your raw data (See configuration) and QuShape projects if you already treated some experiments

Run pipeline

  1. 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 or the version of the Sargueil lab.

  2. 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 :

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

ipasuite log

Will show pipeline scripts log

Clean file

at any point, you can clean pipeline files :

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:

ipasuite log --clean