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installation

BiG-SCAPE installation

⚪ 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
(bigscape) $ 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 (Linux-like systems)

If you use Docker, copy the run_bigscape file from the repository and run it like so:

$ 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.

⚪ Manual installation

If you don't (or can't) use conda, you will need to download all the files from the repository (e.g. from here), download and prepare the Pfam database (see above) and have the following packages installed in your system:

  • 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
  • Fasttree
  • scipy
  • scikit-learn (tested with 0.19.1)
  • NetworkX (v2.x)