BioEnv is a virtual environment for bioinformatics exploration, analysis and research
- Virtual environment for bioinformatics workflow
- Package/dependency management for bioinformatics workflow
- After having installed and set up bioenv on your machine
Create/Initialize a new bio env
bioenv init . myfirstenv
# note . is the specified working directory where you want to setup an env
This command generates a new bioinformatics virtual environment and creates a bioenv.json configuration file in the specified work directory.
Install a new tool
bioenv install gatk
This command installs a new tool into your environment and modifies the config bioenv.json accordingly
Call/Use any tool in your environment Still thinking about how to improve this
bioenv call gatk --java-options "-Xmx4G" [program arguments]
or
bioenv call bwa index ref.fasta
bioenv call samtools faidx ref.fasta
Stop/Quit virtual environment
bioenv quit
Export virtual environment so you can be able to share it with your colleagues
bioenv export