previously compiled) versions of programs and their dependencies that do not conflict with one another. With conda you create virtual environments into which you install binary (i.e. The second problem usually results from the programs having dependencies that conflict with one another. The first problem may be because installation depends on a specific compiler version you do not have, it has dependencies you do not have installed, or it requires versions of dependencies differing from what you have installed. You may have already found that you could not install a particular program, or that adding another program broke one or more previously installed programs. 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. condarc for the miniconda module.Anaconda, Miniconda, Conda, Bioconda – what’s with all of these condas? Anaconda is a full blown python distribution including over 720 open source packages. If you would like to override these defaults, see the Conda docs on managing channels. Starting with minconda module version 4.8.3 we set the default channels (the sources to find packages) to conda-forge and bioconda, which provide a wider array of packages than the default channels do. Conda will install to and search in these directories for environments and cached packages.
On all clusters, we set the CONDA_ENVS_PATH and CONDA_PKGS_DIRS environment variables to conda_envs and conda_pkgs in your project directory where there is more quota available. Note: If you are on Milgram and run out of space in your home directory for Conda, you can either reinstall your environment in your project space (see below) or contact us for help with your home quota. If you are using Conda-installed packages, this should be the only module you load in your jobs. We set some defaults for you in this module, and we keep it relatively up-to-date so you don't have to. This is a read-only environment from which you can create your own. The Miniconda Moduleįor your convenience, we provide a relatively recent version of Miniconda as a module. If you get stuck, you can always ask us for help. When constructing an environment for your work you should load either modules or a conda environment. Mixing modules and conda-managed software is almost never a good idea. Conda version doesn't match the module loaded
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