Bioinformatics Brew

Currently supports:

Ubuntu 14.04,15.10,16.04CentOS 6,7OS X 10.11

Help us expand our support by trying BiB on another OS and reporting any issues.

Installs to /opt/bib

BiB doesn't get in the way of your other software or anything outside of its prefix. It installs each package in a self-contained directory tree, then links the program into /opt/bib/active/bin. Install your Python packages with pip and your non-bioinformatics software with the package manager of your choice.

Install your favorite tools

BiB provides all the common bioinformatics software you would expect, plus specialized tools that are often left out of other package managers and repositories.

$ bib install blast bowtie raxml swipe
$ bib list
Installed packages:
Name         Version   InstallStatus   ActiveStatus
blast        2.2.29+       Installed         Active
bowtie         1.0.0       Installed         Active
raxml          7.7.6       Installed         Active
swipe          2.0.9       Installed         Active

Specify the exact version

And install multiple versions, with one active at a time.

$ bib install blast/2.2.28+ blast/2.2.29+

$ bib activate blast/2.2.29+
$ ls -L `which blastn`
/opt/bib/install/blast/2.2.29+/bin/blastn

$ bib activate blast/2.2.28+
$ ls -L `which blastn`
/opt/bib/install/blast/2.2.28+/bin/blastn

Recipes are simple Python config files

$ cat /opt/bib/recipes/bwa.bb
[default]
name = bwa
homepage = http://bio-bwa.sourceforge.net/
toolchain = inplace
build_cmds = make CC=gcc
bin = bwa
man/man1 = bwa.1

[20140117_v_0.7.5a_v_ALL]
url = http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.5a.tar.bz2
sha1 = 3ba4a2df24dc2a2578fb399dc77b3c240a5a18be

Built on top of git and Bitbucket

Keep up-to-date by simply pulling the latest recipes.

$ bib update
remote: Counting objects: 16, done.
remote: Compressing objects: 100% (9/9), done.
remote: Total 9 (delta 7), reused 0 (delta 0)
Unpacking objects: 100% (9/9), done.
From https://bitbucket.org/mhowison/bib
   b248e44..d066286  master     -> origin/master
 * [new branch]      rsem       -> origin/rsem
   862c469..1ab614f  trinity    -> origin/trinity

Coming soon: build and activate the latest versions.

$ bib upgrade
...