Using ESCOTT via Singularity
============================
You can not run docker on many high performance computing systems
due to sudo permissions etc.
However, singularity can be run on them. Due to this reason, I prepared
this file to show how you can prepare a singulartiy sif file from (online) docker
image of PRESCOTT.

* STEP 0: First thing first! You must have singularity installed on your system.
  
    If not, you can find the installation instructions here:
    https://github.com/sylabs/singularity/blob/main/INSTALL.md

    In addition, there are different releases(deb, rpm or source) in the following page:
    https://github.com/sylabs/singularity/releases

* STEP 1: Building singularity from the docker image online:
 
    .. code:: bash

        singularity build prescott-docker-v1.6.0.sif docker://tekpinar/prescott-docker:v1.6.0

    Please note that you will need to change (v1.6.0) to the version you want if there is an update in the version.

* STEP 2: Running escott with the sif file:

    .. code:: bash

        singularity exec prescott-docker-v1.6.0.sif escott -h

* STEP 3: Running prescott with the sif file:

    .. code:: bash

        singularity exec prescott-docker-v1.6.0.sif prescott -h

* STEP 4: Go to the folder where both aliBLAT.fasta and blat-af2.pdb are located. 
        These two files are provided in the data folder of this repository.
        YOUR_SINGULARITY_DIR is where prescott-docker-v1.6.0.sif file is located. 

    .. code:: bash

        singularity exec --home `pwd` $YOUR_SINGULARITY_DIR/prescott-docker-v1.6.0.sif escott aliBLAT.fasta --pdbfile blat-af2.pdb
