All three of these python distributions include conda, a package and virtual environment manager. Conda installs programs from repositories called channels, and Bioconda is a channel devoted to bioinformatic programs.Ĭonda allows you to solve problems often encountered when installing bioinformatics programs. The minicondas (you probably guessed it) are smaller and do not take up as much drive space because they do not include all of the packages found in Anaconda. Miniconda comes in two versions: Miniconda2 is a python 2.7 distribution while Miniconda3 is a python 3 distribution. This means you can save time and effort in building your images.Anaconda, Miniconda, Conda, Bioconda – what’s with all of these condas? Anaconda is a full blown python distribution including over 720 open source packages. Best of all? It’s only ~13 MiB to download. with no dependency on Conda, and that doesn’t include a default Python version making it perfect for setting up fresh environments with as small a footprint as possible. Micromamba is a standalone binary version of Mamba, i.e. This is where Micromamba comes into play! The download size for the mambaforge package is ~100 MiB, which is a fair bit larger than Miniconda is.įor regular use, this isn’t a big deal, but when you’re trying to create lean docker images in a production environment without requiring lots of space-saving manual intervention, it helps to have as small a download as possible. Because it depends on Conda, either way of installing it means you end up with both package managers on your system. Mamba is definitely faster than Miniconda, but unfortunately it is still quite a wedge to download. This may be important if the computers where your CI jobs are running are particularly weak. In addition, on the smallest instance Miniconda failed to complete its task because it ran out of memory and the process was unceremoniously terminated. This may seem like a significant step down from the massive gains seen previously, but factor this out over a year’s worth of CI runs and one starts to see how this could be beneficial, especially if you’re paying for CI time. In general, even for this relatively small environment, Mamba was approximately half a minute quicker to set everything up. Mamba is most akin to Miniconda, in that it comes with Python, but doesn’t ship with a whole load of extra software. This is where Mamba comes in, the fast drop-in replacement for conda, which reimplements the slow bits in in C++. Whilst Miniconda is small as compared with full-fat anaconda, the latest Miniconda3 Linux 64-bit Python 3.9 download size is 58.6 MiB, could this be better?
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