1 Prepare the environment

The first step is to prepare the C2 environment to smoothly run your data through HoloFlow.

In C2, you need to work in your project-user directory, rather than in your home directory. The path to your user directory is: /home/projects/[group-name]/people/[user-name]

1.1- Install or update HoloFlow

HoloFlow does not require an installation, it is enough to clone it from Github. The HoloFlow folder containing all scripts can be stored in any location, but we advise against installing HoloFlow inside the project directory. In this tutorial we will place it in the main project-user directory.

Go to the directory where you want to place holoflow. e.g.:

cd /home/projects/ku-cbd/people/antalb

If the folder exists, remove before cloning the latest version from Github.

rm -rf holoflow

Clone the latest version from the Github repository. It is important to clone it from the nurher branch, which contains the most updated version of HoloFlow.

git clone -b nurher --single-branch https://github.com/anttonalberdi/holoflow.git

1.2- Prepare the working directory and declare paths

1.2.1 - Create the working project directory

In this example, we will create a folder named holoproject which will contain all the files, data and results that HoloFlow will create.

mkdir /home/projects/ku-cbd/people/antalb/holoproject

1.2.2 - Declare the project paths for HoloFlow and the project directory.

A very useful trick to avoid writing the entire paths, is to declare the two most relevant paths as variables.

workdir=/home/projects/ku-cbd/people/antalb/holoproject
holodir=/home/projects/ku-cbd/people/antalb/holoflow

From now on, any time you type ${workdir} it will mean /home/projects/ku-cbd/people/antalb/holoproject From now on, any time you type ${holodir} it will mean /home/projects/ku-cbd/people/antalb/holoflow

1.2.3 - Create folders to organise files generated during the analysis

HoloFlow will create a considerable number of final files, and MANY intermediate files. Running the different workflows of the suite will also require to prepare many input and config files. Hence, it is important to keep everything properly organised. We suggest creating the following directories:

• input for storing input and config files.
• jobs to store job launching shell files.
• genomes for storing reference genomes.
• rawdata to store raw data files.

The information stored in these folder can be also stored elsewhere. Bear in mind though that if you are using a different path, you will need to change all the downstream commands yourself.

To create the new folders use the following command:

mkdir ${workdir}/input
mkdir ${workdir}/jobs
mkdir ${workdir}/genomes
mkdir ${workdir}/rawdata

Now you are ready to start HoloFlowing!