recipe bbmap

BBMap is a short read aligner, as well as various other bioinformatic tools.

Homepage:

https://sourceforge.net/projects/bbmap

Documentation:

https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/

License:

UC-LBL license (see package)

Recipe:

/bbmap/meta.yaml

Links:

biotools: bbmap, doi: 10.1371/journal.pone.0185056

package bbmap

versions:

39.06-0,  39.01-1,  39.01-0,  39.00-0,  38.99-0,  38.98-1,  38.98-0,  38.97-1,  38.97-0, 

39.06-0,  39.01-1,  39.01-0,  39.00-0,  38.99-0,  38.98-1,  38.98-0,  38.97-1,  38.97-0,  38.96-1,  38.96-0,  38.95-1,  38.95-0,  38.93-0,  38.92-0,  38.91-1,  38.91-0,  38.90-3,  38.90-2,  38.90-1,  38.90-0,  38.89-0,  38.88-0,  38.87-0,  38.86-0,  38.84-1,  38.84-0,  38.79-0,  38.76-0,  38.75-0,  38.73-0,  38.72-0,  38.71-0,  38.70-0,  38.69-0,  38.68-0,  38.67-0,  38.65-0,  38.63-0,  38.62-0,  38.61b-0,  38.58-0,  38.57-0,  38.56-0,  38.51-0,  38.49-0,  38.46-0,  38.45-0,  38.44-0,  38.22-1,  38.22-0,  38.20-0,  38.19-0,  38.18-0,  38.16-0,  38.06-2,  38.06-0,  37.99-1,  37.99-0,  37.96-0,  37.95-0,  37.90-0,  37.78-0,  37.77-0,  37.75-0,  37.66-0,  37.62-2,  37.62-1,  37.62-0,  37.52-1,  37.52-0,  37.17-1,  37.17-0,  37.10-1,  37.10-0,  37.02-0,  36.84-0,  36.32-0,  35.85-2,  35.85-1

depends bzip2:

>=1.0.8,<2.0a0

depends libgcc-ng:

>=12

depends openjdk:

>=7.0

depends pbzip2:

depends samtools:

>=1.19.2,<2.0a0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bbmap

and update with::

   mamba update bbmap

To create a new environment, run:

mamba create --name myenvname bbmap

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bbmap:<tag>

(see `bbmap/tags`_ for valid values for ``<tag>``)

Notes

BBMap is a series of Java programs, but they come with a number of custom wrapper shell scripts. Each of these is symlinked to the conda bin directory during install.

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