Johannes Köster
2016
- provide binary packages of any Bioinformatics software
- fast and easy deployment
- no admin rights
- allow simultaneous usage of multiple versions of the same package
Goals
Already over 1600 packages
(C, C++, Python, R, Perl, ...)
Rapidly growing
Over 100 contributors
Vital community
Integrated with 3 popular workflow management systems
Integration with WMS
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
conda config --add channels r
conda config --add channels conda-forge
conda config --add channels bioconda
Setup
Bioconda is based on the language agnostic Conda package manager
conda install bwa=0.7.15
conda update bwa
conda remove bwa
Isolated environments:
channels:
- r
- conda-forge
- bioconda
dependencies:
- picard ==2.3.0
- samtools ==1.3.0
- bioconductor-deseq2 ==1.10.1
Usage
Recipe with metadata:
package:
name: bwa
version: "0.7.15"
source:
fn: v0.7.15.tar.gz
url: https://github.com/lh3/bwa/archive/v0.7.15.tar.gz
requirements:
build:
- gcc
- zlib
run:
- zlib
test:
commands:
- bwa 2>&1 | grep 'index sequences in the'
about:
home: http://bio-bwa.sourceforge.net
license: MIT
summary: The BWA read mapper.
Packaging made easy
Bash script for compilation:
#!/bin/bash
export C_INCLUDE_PATH=${PREFIX}/include
make
mkdir -p $PREFIX/bin
cp bwa $PREFIX/bin
Packaging made easy
Conda can be used to handle data as well.
Watch out for the upcoming
Go Get Data project:
conda install --channel ggd hg38-dbsnp
Beyond software
Visit
https://bioconda.github.io
Bioconda
By Johannes Köster
Bioconda
Presentation of Bioconda for DTL
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