Dependencies

Dependencies#

WfExS-backend 1.0 source code and its dependencies should be compatible with Python 3.7 and later, including Python 3.12.

Local dependencies#

When installing WfExS-backend locally on your system, certain dependencies are required to ensure proper functionality. These dependencies include software, libraries, and tools that the application relies on for execution. This section outlines the requirements on your local environment before proceeding with the installation, helping to avoid compatibility issues or missing functionality.

Core dependencies#

Before starting the installation process, please check whether your system has all the necessary dependencies. In order to install the dependencies you need pip and `venv`_ Python modules, and the essential build dependencies.

Ensure the following prerequisites are installed:

  • git

  • curl

  • tar

  • gzip

  • build-essential package in Linux systems (installation steps here). Essential build dependencies (gcc, make, …) are provided in Ubuntu with build-essential package.

  • python3 (Python 3.7 or later)

  • pip: available in many Linux distributions (Ubuntu packages python3-pip, CentOS EPEL package python-pip), and also as pip Python package.

  • venv: available in many Linux distributions (Ubuntu package python3-venv). In some of them is integrated into the Python 3.5 (or later) installation.

These components are essential for the successful execution of the installation script. Once you have verified and installed all the required dependencies, you can proceed with the local installation of WfExS on your system. If any of the dependencies is missing, install them on your system before proceeding further.

Software dependencies#

WfExS-backend requires additional software dependencies beyond the core ones to facilitate various stages of the code execution. Depending on your workflow local configuration, some other external tools or container technologies are needed in several stages of the code. Please, install them, using either native packages (for instance, from your Linux distribution) or by hand and later set their path in the local configuration file you are using. Ensure that these dependencies are properly configured.

git

Required to fetch workflows from git repositories.

libmagic.so

Dynamic library from file package is needed by python-magic package.

dot

Command (from GraphViz) is needed to generate a graphical representation of workflows on Workflow Run RO-Crate generation.

Container technologies:

docker

Required when local installation is set up to use Docker. Note that not all combinations of workflow execution engines and secure or paranoid setups support Docker.

podman

Required when local installation is set up to use Podman. Note that not all combinations of workflow execution engines and secure or paranoid setups support Podman.

singularity or apptainer

Required when local installation is set up to use Singularity. Needed version 3.5 or later. Singularity and Apptainer depend on mksquashfs, available in Ubuntu through the squashfs-tools package.

To install singularity or apptainer at WfExS-backend virtual environment (.pyWEenv), if you use Ubuntu Linux, a rootless setup is achieved using either singularity-local-installer.bash or apptainer-local-installer.bash. At most only one of them can be locally installed, because as of September 2022 workflow engines like cwltool or nextflow still use the hardcoded name of singularity. So, the apptainer installer has to create a singularity symlink pointing to apptainer.

container_recipes/singularity-local-installer.bash

container_recipes/apptainer-local-installer.bash

Workflow engines prerequisites:

java

Necessary for running Nextflow. Supported Java versions range from 8 to any version below 15 (Nextflow does not support version 15). Both OpenJDK and Sun implementations should work.

Secure environment:

gocryptfs

Securing intermediate results. Tested since version v2.0-beta2; releases provide static binaries.

encfs

Securing intermediate results. Tested with versions 1.9.2 and 1.9.5; releases need to be compiled or installed from your distribution.

Secure working directories limitations#

Currently, both Nextflow and cwltool support secure and paranoid working directories when no container technology is set up.

  • When singularity / apptainer mode is set up, both Nextflow and cwltool support secure working directories when either singularity was compiled and set up with user namespaces support, or FUSE was set up at the system level in /etc/fuse.conf with the flag user_allow_other.

  • When docker or podman are set up, there is no support for secure or paranoid working directories due technical and architectural limitations.