StrainEst - Docker
StrainEst is a reference-based method that leverages on the accumulated knowledge of the genomic variability of species of interests to identify individual strains and quantify their relative abundances in mixed metagenomic samples.
Sickle, Bowtie2 and samtools are preinstalled.
- latest: GitHub snapshot (master)
- 1.2.1: strainest 1.2.1
Download the latest version:
docker pull compmetagen/strainest
Run an instance of the image, mounting the host working directory
/Users/davide/strainest) on to the container working directory
docker run --rm -t -i -v /Users/davide/strainest:/strainest -w /strainest compmetagen/micca /bin/bash
You need to write something like
you are in Windows or
-v /home/davide/strainest:/strainestin Linux. The
--rmoption automatically removes the container when it exits.
Run micca without parameters:
root@68f6784e1101:/strainest# strainest --help