What else can we use Conda for?¶
Reproducing analyses¶
Why: removes the guesswork on what version of software to use or how to install it!
For example, it's a lot easier to replicate a software environment from a publication or share software versions used in your own analysis using conda (particularly with methods 3 & 4, mentioned previously, to create conda environments from YAML or exact package list files).
Packaging software¶
Why: to share your cool software with the world!
The gist is that you write a recipe that has all the specifications about your software that is submitted to a channel, e.g., conda-forge or bioconda. Once correctly formatted and tested (with continuous integration automation) so it works on different operating systems, it's added to the channel and the world can use and install your software with conda!
Running parts of analysis workflows in their own environment¶
Why: avoid software version conflicts, easier to keep track of software/versions used for a specific analysis, easier for others to reproduce
This is a very helpful feature for workflows. For example, in Snakemake workflows, you can specify that each step (called a "rule") is executed in an isolated conda environment by adding a conda: directive:
rule fastqc_raw:
input: "rnaseq/raw_data/{sample}.fq.gz"
output: "rnaseq/raw_data/fastqc/{sample}_fastqc.html"
params:
outdir="rnaseq/raw_data/fastqc"
conda: "rnaseq-env.yml"
shell:
"""
fastqc {input} --outdir {params.outdir}
"""
Creating binders¶
Why: teaching tool for software or analysis demos, share reproducible analysis
Examples:
-
the Rstudio binder we used for this lesson was created with https://binder.pangeo.io/
-
Metabolomics Workbench metENP binder: tool for metabolite enrichment analysis and their associated enriched pathways