The biolibc library is new and evolving rapidly. It will likely undergo occasional API changes as we discover suboptimal design decisions that have made it into the implementation.
API changes will become less frequent as the software matures. For now, be prepared to update dependent software in order to stay with the latest biolibc.
Keep in mind that older releases are always available on Github, so API changes won't impact you by surprise. You only need to deal with them when updating to a newer version of biolibc.
Many bioinformatics pipelines are essentially made of mud and straw; quick-and-dirty single-use scripts written in various interpreted languages, with little or no meaningful error reporting or documentation, and generally poor performance.
Biolibc is a collection of high-quality bricks that can be used to build efficient, robust software applications to replace disposable scripts. Using biolibc, you can easily develop permanent solutions that are easy to use and install, with near-optimal performance, so that no one ever need reinvent that particular wheel. Biolibc also facilitates development of more complex applications by providing many commonly used building blocks, thus releasing you from low-level coding.
For some examples, see biolibc-tools, vcf-split, ad2vcf, vcf2hap, haploh-vcf-depths, peak-classifier, generand, ad-matrix, fastq-trim and FASDA.
In more technical terms, biolibc is a library of fast, memory-efficient C functions for processing biological data. Like libc, it consists of numerous disparate, general-purpose functions that can be used by a wide variety of applications.
These include classes for reading, writing, and manipulating common file formats such as BED, GFF, FASTA, FASTQ, SAM and VCF, string functions specific to bioinformatics such as chromosome_name_cmp(), functions to detect feature overlaps, etc.
Biolibc, and the more generic libxtend, move your C coding to a higher level by providing the most basic building blocks and additional software layers commonly needed in bioinformatics programming. Using C and biolibc, you can write simple, near-optimal C programs that may be orders of magnitude faster than scripting languages such as Perl, Python, and R, while requiring comparable coding effort. fastx-derep.c, a 1-page C program for dereplicating FASTA/FASTQ files, offers a great example of how the right libraries eliminate the need for low-level programming in C.
See the Research Computing User's Guide Compiled vs Interpreted Languages section for a comparison of language performance.
This function summary lists currently available API functions. It is also available via "man biolibc" when biolibc is properly installed via a package manager. Each function listed has its own man page with a more detailed description.
The code is organized following basic object-oriented design principals, but implemented in C to minimize overhead and keep the source code accessible to scientists who don't have time to master the complexities of C++.
Structures are treated as classes, with accessor macros and mutator functions provided, so dependent applications and libraries need not access structure members directly. Since the C language cannot enforce this, it's up to application programmers to exercise self-discipline.
For detailed coding standards, see https://github.com/outpaddling/Coding-Standards/.
biolibc is intended to build cleanly in any POSIX environment on any CPU architecture. Please don't hesitate to open an issue if you encounter problems on any Unix-like system.
Primary development is done on FreeBSD with clang, but the code is frequently tested on Linux, MacOS, NetBSD, and OpenIndiana as well. MS Windows is not supported, unless using a POSIX environment such as Cygwin or Windows Subsystem for Linux.
The Makefile is designed to be friendly to package managers, such as Debian packages, FreeBSD ports, MacPorts, pkgsrc, etc. End users should install using a package manager. Note that pkgsrc can be used by anyone, on virtually any POSIX operating system, with or without administrator privileges..
I maintain a FreeBSD port and a pkgsrc package, which is sufficient to install cleanly on virtually any POSIX platform. If you would like to see a biolibc package in another package manager, please consider creating a package yourself. This will be one of the easiest packages in the collection and hence a good vehicle to learn how to create packages.
For an overview of available package managers, see the Repology website.
FreeBSD is a highly underrated platform for scientific computing, with over 2,000 scientific libraries and applications in the FreeBSD ports collection (of more than 30,000 total), modern clang compiler, fully-integrated ZFS file system, and renowned security, performance, and reliability. FreeBSD has a somewhat well-earned reputation for being difficult to set up and manage compared to user-friendly systems like Ubuntu. However, if you're a little bit Unix-savvy, you can very quickly set up a workstation, laptop, or VM using desktop-installer. GhostBSD offers an experience very similar to Ubuntu, but is built on FreeBSD rather than Debian Linux. GhostBSD packages lag behind FreeBSD ports slightly, but this is not generally an issue and there are workarounds.
To install the binary package on FreeBSD:
pkg install biolibc
You can just as easily build and install from source. This is useful for FreeBSD ports with special build options, for building with non-portable optimizations such as -march=native, and for work-in-progress ports, for which binary packages are not yet maintained.
cd /usr/ports/biology/biolibc && env CFLAGS='-march=native -O2' make install
cd /usr/ports/wip/biolibc && make install
pkgsrc is a cross-platform package manager that works on any Unix-like platform. It is native to NetBSD and well-supported on Illumos, MacOS, RHEL/CentOS, and many other Linux distributions. Using pkgsrc does not require admin privileges. You can install a pkgsrc tree in any directory to which you have write access and easily install any of the nearly 20,000 packages in the collection.
The auto-pkgsrc-setup script will help you install pkgsrc in about 10 minutes. Just download it and run
sh auto-pkgsrc-setup
Then, assuming you selected current packages and the default prefix
source ~/Pkgsrc/pkg/etc/pkgsrc.sh # Or pkgsrc.csh for csh or tcsh
cd ~/Pkgsrc/pkgsrc/biology/biolibc
sbmake install clean clean-depends
See the pkgsrc documentation for more information.
Community support for pkgsrc is available through the pkgsrc-users mailing list.
Packages for libxtend are known to exist in the following package managers. These are maintained by third parties and not directly supported here.
If you would like to add this project to another package manager rather than use FreeBSD ports or pkgsrc, basic manual build instructions for package can be found here. Your contribution is greatly appreciated!