The cross-platform package manager for open-source bioinformatics tools.
Help us expand our support by trying BiB on another OS and reporting any issues.
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.
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
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
$ 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
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 ...