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How to Install ?

Hereafter, you will find all the details about the intronSeeker installation.

Requirements

IntronSeeker requires Python version 3.6 or above. You don't need to change your Python version because this is managed by your Conda environment.

It also needs Python packages and external softwares to work correctly (all these dependancies and their versions are detailed in the file requirements.txt). So, to make install easier, a conda enviromnent (grinder excluded) has been created : Conda environment (it is the environment.yml file)

For an easy install, creating a conda environment is recommended. Follow this tutorial to install Miniconda. For a faster installation, we advise you to use mamba, already available in the latest version of conda

intronSeeker installation and environment configuration on genobioinfo

First, open a bash session if you are not already in bash (bash command).

Clone intronSeeker code from Git.

Download all files and directories found at URL

$ git clone https://github.com/Bios4Biol/intronSeeker.git
Cloning into 'intronSeeker'...
remote: Enumerating objects: 2364, done.
remote: Counting objects: 100% (2334/2334), done.
remote: Compressing objects: 100% (798/798), done.
remote: Total 2364 (delta 1538), reused 2313 (delta 1523), pack-reused 30
Receiving objects: 100% (2364/2364), 539.80 MiB | 54.32 MiB/s, done.
Resolving deltas: 100% (1556/1556), done.
Checking out files: 100% (153/153), done.

Install intronSeeker environment.

$ cd intronSeeker
$ conda env create -f config/environment.yml

You can speedup intronSeeker installation by using mamba or libmamba

Activate ISeeker_environment and test installation.

Before each use of intronSeeker, activate the conda environment with :

$ conda activate ISeeker_environment

Now, your command prompt should be like this :

(ISeeker_environment) [...]$

Finally, to test the installation, run the command :

(ISeeker_environment) $ ./intronSeeker checkInstall

You should get this message in standard ouput :

gffread testing...OK ! 

grinder testing...OK ! 

hisat2 testing...OK ! 

star testing...OK ! 

samtools testing...OK ! 

transdecoder testing...OK ! 

diamond testing...OK ! 

All the dependencies are correctly installed

To see intronSeeker help:

(ISeeker_environment) $ ./intronSeeker -h

Program: intronSeeker
Version: 1.0

Add intronSeeker into you conda env PATH (once)

intronSeeker can be run from anywhere. In order to avoid to type the full PATH to intronSeeker program, you can create a symbolic link into the ISeeker_environment environment. You can use the following command when ISeeker_environment environment is loaded to do this:

ln -s "${PWD}"/intronSeeker "${CONDA_PREFIX}/bin/"

Then you can run it from anywhere:

(ISeeker_environment) $ intronSeeker -h

Program: intronSeeker
Version: 1.0