![]() ![]() This installs CNVkit plus the appropriate Python and R dependencies. Packages can then be installed using conda install cnvkit Whilst there are a number of compilaions of Bioinformatics software, Bioconda looks to be by far the most comprehensive.Īfter installing Conda, the first step is to set up the Bioconda channel conda config -add channels conda-forge You can read more details in this publication "Bioconda: A sustainable and comprehensive software distribution for the life sciences", doi. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges. To start things rolling I've added PubChem.py to Bioconda and I've written a page describing how to create a bioconda recipe.īioconda is a channel for the conda package manager specializing in bioinformatics software.īioconda supports only 64-bit Linux and Mac OSX.īioconda offers a collection of over 2900 software tools, which are continuously maintained, updated, and extended by a growing global community of more than 250 contributors. If you do package a chemistry application for Bioconda please let me know and I'll publicise it on my blog and add it to the list above. Rather than try to duplicate this effort for a "Chemconda" it seems more efficient to encourage chemists to contribute to Bioconda. These include:īioconda offers a collection of over 3100 software tools, which are continuously maintained, updated, and extended by a growing global community of more than 330 contributors. Looking through the packages it is clear there it already contains a number of chemistry packages. The bioconda channel is a Conda channel providing bioinformatics related packages for Linux and Mac OS. Conda is both language- and OS-agnostic, and can be used to install C/C++, Fortran, Go, R, Python, Java etc Conda is a combination of other package managers you may have encountered, such as pip, CPAN, CRAN, Bioconductor, apt-get, and homebrew. The conda package manager has recently made installing software a vastly more streamlined process. Conda is a platform- and language-independent package manager that sports easy distribution, installation and version management of software. You can read more details in this publication "Bioconda: A sustainable and comprehensive software distribution for the life sciences", DOI. This project is licensed under the MIT LicenseĪ little while back I mentioned BioConda. The GitHub page contains detailed instructions for installation. if topology provided, interaction energy grids can be calculated for transient pockets and channels (experimental). ![]() can now read Gromacs XTC, netcdf and dcd trajectories.Yields now slightly better results than the original implementation. druggability score has been reoptimized vs original paper.pocket flexibility using temperature factors is better considered (less very flexible pockets on very solvent exposed areas).is now able to consider explicit pockets when you want to calculate properties for a known binding site.What's new compared to fpocket 2.0 (old sourceforge repo) The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. ![]()
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