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BiG-SCAPE
BiG-SCAPE

installation

Last edited by Jorge Navarro Muñoz
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BiG-SCAPE installation

Requirements

  • Python (BiG-SCAPE development will focus on Python 3. We will try to keep compatibility with Python 2 as long as we can)
  • The HMMER suite (3.1b2+)
  • The Pfam database
  • Biopython
  • Numpy
  • scipy
  • scikit-learn (tested with 0.19.1)
  • NetworkX (v2.x)

Installation using conda

Copy the latest version of the BiG-SCAPE repository:

  • Option 1: Clone the repository if you have git
$ git clone https://git.wur.nl/medema-group/BiG-SCAPE.git
  • Option 2: Download and decompress the current version of the code. In a terminal, this would be done with:
$ wget https://git.wageningenur.nl/medema-group/BiG-SCAPE/-/archive/master/BiG-SCAPE-master.zip
$ unzip BiG-SCAPE-master.zip && mv BiG-SCAPE-master/ BiG-SCAPE/

Although each library could be installed on its own, the use of a virtual environment is highly recommended. Here is a quick guide of BiG-SCAPE installation using Miniconda

Install Miniconda.

We recommend that you install the Python 3 version as default for all new conda environments.

$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh

Create a new environment and install all the packages listed above using the environment.yml file (see additional documentation about conda here).

$ conda env create -f environment.yml

Activate new environment (you should see a change in the prompt)

$ source activate bigscape
(bigscape) $

Prepare the Pfam database

For simplicity, it will be put in the same BiG-SCAPE folder but it can be located elsewhere. BiG-SCAPE has been tested with versions 31 and 32, and newer versions should work fine. Note that in this example, version 32 is used. Browse the different versions here.:

(bigscape) $ cd BiG-SCAPE
(bigscaep) $ wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/Pfam-A.hmm.gz && gunzip Pfam-A.hmm.gz 
(bigscape) $ hmmpress Pfam-A.hmm

Run BiG-SCAPE:

(bigscape) $ python bigscape.py --version

(see here for an overview of the options)

To deactivate the environment do source deactivate.

Docker

If you use Windows or want a simple method to run BiG-SCAPE, install Docker, copy the run_bigscape file from the repository and run it:

$ mkdir ~/bin # not required if you already have that
$ curl -q https://git.wageningenur.nl/medema-group/BiG-SCAPE/raw/master/run_bigscape > ~/bin/run_bigscape
$ chmod a+x ~/bin/run_bigscape
$ ~/bin/run_bigscape

See the combined BiG-SCAPE/CORASON website for more detailed instructions and an example.