1. Installation

In order to install Bioconvert, you can use the pip method but you may not get all functionalities available. Instead, we recommend bioconda that will install the Python dependencies as well as the third-party packages.

Bioconvert depends on many external resources and we therefore recommend the bioconda method that installs pre-compiled libraries.

1.1. pip installation

For users, Bioconvert can be installed with the pip tool as follows:

pip install bioconvert

This method installs Bioconvert and its Python dependencies. Note, however, that bioconvert may use (depending on the conversion you want to use) external dependencies not available on Pypi. You will need to install those third-party dependencies yourself. An alternative is to install bioconvert using conda as explained here after

1.2. conda / bioconda installation

You can install Bioconvert and its dependencies with conda as follows:

conda install bioconvert

Note that you will need to set up the bioconda channel (see below for details).

conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

Warning

it is important to add them in this order, as mentionned on bioconda webpage (https://bioconda.github.io/).

If you have already set the channels, please check that the order is correct. With the following command:

conda config --get channels

You should see:

--add channels 'r'   # lowest priority
--add channels 'defaults'
--add channels 'conda-forge'
--add channels 'bioconda'   # highest priority

1.3. From source

For developers, if you want to use the latest source files and based on bioconda to install the dependencies you just need to do:

git clone https://github.com/bioconvert/bioconvert
cd bioconvert
conda install --file requirements.txt
conda install --file requirements_tools.txt
conda install --file requirements_dev.txt
python setup.py install

1.4. Singularity

For production, we would recommend to use the singularity container.

This method will download a file (container) with everything pre-compiled and pre-installed with the latest version available on Pypi.

First, you will need to install singularity. To install the version 2.4 of singularity on a Linux plaform, just download and execute this install_singularity.sh bash script, or just type these commands:

VERSION=2.4
wget https://github.com/singularityware/singularity/releases/download/$VERSION/singularity-$VERSION.tar.gz
tar xvf singularity-$VERSION.tar.gz
cd singularity-$VERSION
./configure --prefix=/usr/local
make
sudo make install

Note

here we need to be sudo, but you can install singularity localy if needed.

For other version, or to install singularity on windows or Mac, please check out the singularity website http://singularity.lbl.gov/

First, download the container. For the latest version:

singularity pull --name bioconvert.img shub://bioconvert/bioconvert:latest

or for a specific version:

singularity pull --name bioconvert.img shub://bioconvert/bioconvert:0_3_0

You can then create an alias:

alias bioconvert="singularity run bioconvert.simg bioconvert"