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Dr Sascha Ott - APPLES


Introduction

The APPLES (Analysis of Plant Promoter-Linked Elements) software package is a set of tools to analyse promoter sequences on a genome-wide scale.

On this page, we provide different versions of the software for download. APPLES is a complex library of Perl functions which has many dependencies, we therefore recommend downloading our VirtualBox appliance as the easiest way of getting started.

Virtualbox Appliance

We are providing a virtual machine running the APPLES software, which includes all dependencies required. The virtual machine image is based on Ubuntu Server 12.04 and includes copies of the Ensembl Perl API Code, as well as of the seaweeds alignment plot code. To use this virtual machine image, you will need to download a copy of Oracle © Virtualbox that runs on your preferred operating system. After installing Virtualbox, you will need to follow these steps for starting up the virtual machine:

  1. Ensure you are using a computer which has enough RAM (>=4GB are recommended, the VM is set up to use 1GB) and hard disk space (the VM hard disk image is limited to 16GB).
  2. Download the virtual machine image (LARGE FILE): [APPLESVM-1.0.ova] (3.3GB)
  3. Unpack the image on your machine and import it into Virtualbox using the "File → Import Appliance" menu item.
  4. Start the virtual machine. The login screen will show further instructions:
    APPLES VM
  5. You can try out some of our example scripts (see http://www.wsbc.warwick.ac.uk/peterkrusche/APPLES/docs/EXAMPLES.md.html for a full list of examples to try). This one will compute conserved regions in Arabidopsis non-coding sequences:
    cd ~/VM/remos
    perl phylo_remos_testing.pl

    The results from this script will be appended to the FASTA files in ~/VM/remos/remos. Pre-computed results are available in ~/VM/remos/0.7.

    Alternatively, you can try some of the test scripts in ~/VM/sample_user_scripts_regression_tests. These scripts leave their output in ~/VM/sample_user_scripts_regression_tests/output_directory.

    cd ~/VM/sample_user_scripts_regression_tests
    perl build_a_ReRe_Set.pl
  6. In order to access the virtual machine via alternative interfaces to run and edit scripts or to browse files you can connect to the virtual machine via SSH (on port 10002, user name "applesuser", password "apples123").

Known issues (15/07/2012):

  • The output of phylo_remos_testing.pl may differ slightly from the precomputed results in ~/VM/remos/0.7, since it uses a slightly different default parameter set.
  • Some of the examples require access to our motif database server (BiFa) and will not work unless you have access.

See our Updates Page for more information.


APPLES Software Sources and Manual

If you would just like to download the APPLES source code, you can get it here:

[APPLES_11092012.zip] (40MB)

You can browse the APPLES documentation online at

http://www.wsbc.warwick.ac.uk/peterkrusche/APPLES/docs

We also provide a manual which covers some installation instructions, software design principles, relevant information on organising large computations with APPLES using the job handling system, etc.:

[APPLES_manual.pdf] (580kb)

We recommend using the virtual machine download above as a template for a local installation of APPLES.

Feel free to contact Sascha Ott for any questions regarding the setup and development of APPLES.

Ensembl Databases

The virtual machine contains four Ensembl SQL databases, which you can download separately here: