Biobox to run VALET read based assembly evaluation

Bioboxes, http://bioboxes.org/, provide a consistent interface to common bioinformatic tools such as assemblers. This repository contains files needed to build a biobox for the VALET read-based assembly validation tool.

Building VALET Biobox

build with

sudo docker build --tag=valet .

Running the VALET Biobox

Create input, output, and (optionally) cache directories, mount accordingly choose task to be run (default).

To run VALET using the biobox a biobox.yaml file is required. You can use the biobox.yaml file in the "Testing the VALET Biobox" section as a template.

sudo docker run --volume="$(pwd)/input:/bbx/mnt/input:ro" \
                --volume="$(pwd)/output:/bbx/mnt/output:rw" -v cache:/bbx/mnt/cache:rw valet default

Testing the VALET Biobox

You can test the Biobox using test data from the VALET repository, https://github.com/marbl/VALET, and the following biobox.yaml file. After generating the biobox.yaml file and downloading the test data you can run VALET on the test data using the command in the Running the VALET Biobox section, making sure that the input directory contains the biobox.yaml and test data files.

Test Biobox.yaml

---
version: "0.2.0"
arguments:
  assemblies:
    - id: "reference"
      type: contig
      path: "/bbx/mnt/input/c_rudii_reference.fna"
    - id: "relocation"
      type: contig
      path: "/bbx/mnt/input/c_rudii_relocation.fna"
    - id: "dup"
      type: contig
      path: "/bbx/mnt/input/c_rudii_dup.fna"
    - id: "reloc_dup"
      type: contig
      path: "/bbx/mnt/input/c_rudii_reloc_dup.fna"
  reads:
    - id: "test_reads"
      type: "paired"
      path: "/bbx/mnt/input/lib1.fq.gz"

Downloading Test files

You can use the following code to download the test data from the VALET repository.

!/usr/bin/sh
#### Downloading test assemblies

# Reference sequence
wget https://raw.githubusercontent.com/marbl/VALET/master/test/c_rudii_reference.fna
# Simulated duplication error
wget https://raw.githubusercontent.com/marbl/VALET/master/test/c_rudii_dup.fna
# Simulated relocation error
wget https://raw.githubusercontent.com/marbl/VALET/master/test/c_rudii_relocation.fna
# Simulated relocation and duplication error
wget https://raw.githubusercontent.com/marbl/VALET/master/test/c_rudii_reloc_dup.fna

#### Downloading test sequences
wget --output-document lib1.fq.gz https://github.com/marbl/VALET/blob/master/test/lib1.fq.gz?raw=true