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saccharis / SACCHARIS_2

CLI and GUI based bioinformatics pipeline to automate phylogenetic analysis of CAZyme families in FASTA sequences.
GNU General Public License v3.0
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SACCHARIS 2.0

Sequence Analysis and Clustering of CarboHydrate Active enzymes for Rapid Informed prediction of Specificity (SACCHARIS), is a python based pipeline designed to improve functional predictions of uncharacterized sequences for any CAZyme or CBM family currently maintained on the CAZy website or within user-defined datasets through phylogenetic methods.

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Citation

Fraser, A.S.C. et al. (2024). SACCHARIS v2: Streamlining Prediction of Carbohydrate-Active Enzyme Specificities Within Large Datasets. In: Lisacek, F. (eds) Protein Bioinformatics. Methods in Molecular Biology, vol 2836. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-4007-4_16

Documentation

Usage documentation is described in the publication, as well as on the github wiki.

Developer documentation is on github pages: https://saccharis.github.io/SACCHARIS_2/

Installation

Installation guides

Step by step installation guides are available on the github wiki.

Supported Platforms

Currently, linux is the main target platform. It also works on macOS without apple silicon (some of the dependencies such as HMMER are not yet available for apple silicon, but you may get it working under a virtual machine), but be aware that the developer has minimal macOS resources and there is less testing on macOS. Windows installation is possible using the CLI method inside a WSL2 linux environment. If you have a current version of WSL2 and Windows 10/11, you can even launch the gui through WSL2 if graphics is enabled for your WSL2. Installation on base windows is possible but requires several dependencies to be installed and available in the base WSL2 environment (SACCHARIS won't be able to know anything about virtual environments in your WSL environment) and should only be attempted by advanced users familiar with using a CLI, linux/WSL2, conda, bioconda, etc.

Beta installation

Installation option 1: Conda CLI Install

This is the preferred method for most users, since installation should be relatively simple.

First make sure you have installed conda. I recommend downloading a version appropriate to your OS from https://www.anaconda.com/products/distribution#Downloads. Other options include installing miniconda or mamba. The mamba package manager is considerably faster than conda at installing software, particularly helpful for older or less powerful hardware, but as it is a third party reimplementation of conda it may not be available in all institutional settings and comes with no support from the anaconda organization.

Once conda is installed, you have to add the bioconda channel to be able to download SACCHARIS, instructions from https://bioconda.github.io/ are reproduced below.

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

It's recommended to install SACCHARIS into a dedicated virtual environment to avoid compatibility issues with other software. You can learn more about using the conda package manager and virtual environments here:

https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html

With conda installed and the bioconda channel set up, you can easily install SACCHARIS directly into a dedicated virtual environment on the command line with:

conda create -n saccharis_env saccharis

Alternately, you can activate an environment of your choice then download and install SACCHARIS with:

conda install saccharis

Once SACCHARIS is installed you can start the software from command line with saccharis and you can start the gui with saccharis-gui.

Installation option 2: Anaconda navigator GUI installation

If you prefer to use a GUI to install and launch SACCHARIS, you can install SACCHARIS through the anaconda navigator GUI. Install and launch navigator as per https://docs.anaconda.org/free/navigator/, then it's recommended to create a new environment to install saccharis into in the environment tab at the left. You will need to add the bioconda channel to install SACCHARIS, which can easily be done by clicking the "channels" button near the top of the window. Then just search the packages for SACCHARIS and you should be able to install it. Once installed, it should show up as a launchable application in the Home tab with the environment it was installed into selected.

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Installation option 3: Manually install requirements and python package

This is an advanced method of installing SACCHARIS that is not recommended for most users. I would not recommend this unless you are installing in an environment that does not support conda package and environment management, such as a computing cluster.

If you would prefer to install and manage dependencies through another method than the conda environment, this is the explicit list of requirements SACCHARIS 2 needs to function.

All of the following programs installed and available on $PATH variable:

After installing the binary dependencies, you can directly install the python package tarball with pip. This is a useful installation method in a scientific compute cluster where bioinformatics software is already available.

Other versions of the above software may work, but have not been tested extensively.

Installation option 4: Windows Installation

If you have WSL2, it is STRONGLY RECOMMENDED to simply install it on WSL2 with the CLI method above. If you enable GUI support, you can even run the saccharis-gui through recent versions of WSL2. Microsoft has an introduction to installing and using WSL2 here: https://learn.microsoft.com/en-us/windows/wsl/about

We are working on making this easier. Bioconda does not support windows officially at the moment, so we might release a windows version on conda-forge at some point. Basically you have to manually install all the dependencies similar to option 3, but on both your Windows environment AND WSL environment. Even this is slightly broken right now and requires a lot of manual steps, so right now we simply do not recommend doing this. If you must do this because your organization does not support updating to WSL2, please reach out to the developer for installation advice.

Running SACCHARIS

Detailed usage documentation is described in the publication and github wiki for manual usage, or the developer docs for scripted usage.

GUI

You can launch the gui from the command line via saccharis-gui or it can be launched from the anaconda navigator (if navigator is installed).

CLI

In terminal follow usage directions as given by

License

This software is distributed under the terms of the GPL, version 3, excepting that:

Developer Contact

You can contact Alex Fraser at alexscf@msl.ubc.ca for information about the software.

If you encounter bugs, please use the github issue tracker tools to submit bug reports instead of emailing, as it is easier to track that way.