|Latest Version| |License| |DOI| |image3|

|image4|

Databases dependencies
----------------------

The docker image can be used to carry out the analysis by APRICOT which
comprise of the the main software and the required tools.

Additionally users are required to establish a repository containing all
the databases/datasets in a directory ``source_files``.

This can be carried out by using the sheel script
`docker\_support.sh <https://raw.githubusercontent.com/malvikasharan/APRICOT/master/shell_scripts/docker_support.sh>`__
either locally or inside the docker container, which creates the
directory with subfolders as illustrated below.

::

    $ wget https://raw.githubusercontent.com/malvikasharan/APRICOT/master/shell_scripts/docker_support.sh
    $ sh docker_support.sh

::

    source_files
        └───├domain_data            # Location for the files containing keywords for domain selection and subsequently selected domains
        |
        └───├emboss                 # EMBOSS package containing needle software
        |
        └───├reference_db_files
                └───├all_taxid                      # Taxonomy ids for the reference of proteome analysis
                └───├blast                          # BLAST package containing required executables
                └───├cdd                            # Cdd related reference files
                |   └───├Cdd                        # Cdd database (Not required for the tutorial)
                |   └───├cdd_annotation_data        # Cdd related annotation file
                └───├pdb                            # All pdb structures as a reference for the tertiary structures
                └───├pfam                           # Pfam annotation data
                └───├interpro                       # InterPro related reference files
                |   └───├interproscan               # Interpro database and InterProScan related tools (Not required for the tutorial)
                |   └───├interpro_annotation_data   # interPro related annotation files
                └───├go_mapping                     # GO related data containing GO anotation for the domains obtained from CDD and InterPro 

.. |Latest Version| image:: https://img.shields.io/pypi/v/bio-apricot.svg
   :target: https://pypi.python.org/pypi/bio-apricot/
.. |License| image:: https://img.shields.io/pypi/l/bio-apricot.svg
   :target: https://pypi.python.org/pypi/bio-apricot/
.. |DOI| image:: https://zenodo.org/badge/21283/malvikasharan/APRICOT.svg
   :target: https://zenodo.org/badge/latestdoi/21283/malvikasharan/APRICOT
.. |image3| image:: https://images.microbadger.com/badges/image/malvikasharan/apricot.svg
   :target: https://microbadger.com/images/malvikasharan/apricot
.. |image4| image:: https://raw.githubusercontent.com/malvikasharan/APRICOT/master/APRICOT_logo.png
   :target: http://malvikasharan.github.io/APRICOT/