BioBuilds 2017.11

BioBuilds 2017.11 is the second major release of 2017. This release uses the conda package manager and builds on the 2017.05 release by adding 12 packages and updating 22 existing ones. Please refer to the “Applications in BioBuilds 2017.11” table below for more details.

 

This release includes the “biobuilds-opt” package for Linux on x86_64 and Linux on POWER originally introduced in the 2017.05 release. This package adds the “opt” feature into your BioBuilds conda environment, which then causes the conda package manager to preferentially install “alternative” builds of selected built using the hardware vendor’s development toolchain (Intel Parallel Studio XE for x86_64 and IBM Advance Toolchain 10.0 for POWER). In most cases, such builds provide better performance than their counterparts built using the standard gcc-based toolchain.

This release also marks the start of our migration to building packages using the Anaconda 5 toolchains rather than OS-supplied ones. This switch lets us make use of newer compiler capabilities, particularly with regards to performance and security, while keeping support for older operating systems (e.g., CentOS/RedHat 6). It also allows us to reduce the need on external (i.e., OS-provided) dependencies, such as X11 shared libraries.

After installing conda, you can install BioBuilds 2017.11 by running:

The above command will install the “opt”-enabled versions of various tools, if available. If, for some reason, you prefer _not_ to use “opt”-enabled tools, simply omit the “biobuilds-opt” package from the `conda create` command; i.e.,

 

Adding “/path/to/biobuilds-2017.11/bin” to your $PATH environment variable (for example, by setting it in your ~/.bash_profile) will then allow you to run BioBuilds applications without providing a full path. Please refer to the “BioBuilds 2017.11 Release Notes” for additional information about other installation options(including partial installs) and required system libraries.

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