Docker Container Installation and Overview

We have provided a complete installation of the Immcantation framework, its dependencies, accessory scripts, and IgBLAST in a Docker. The image also includes both the IgBLAST and IMGT reference germline sets, as well as several template pipeline scripts. The image is available on docker hub at:

kleinstein/immcantation

Images are versioned through tags with images containing official releases denoted by meta-version numbers (x.y.z). The devel tag denotes the latest development (unstabled) builds.

Getting the Container

Requires an installation of Docker 1.9+ or Singularity 2.3+.

Docker

# Pull release version 2.2.0
docker pull kleinstein/immcantation:2.2.0

# Pull the latest development build
docker pull kleinstein/immcantation:devel

Singularity

# Pull release version 2.2.0
IMAGE="immcantation-2.2.0.img"
singularity create --size 6000 $IMAGE
singularity import $IMAGE docker://kleinstein/immcantation:2.2.0

What’s in the Container

Accessory Scripts

The following accessory scripts are found in /usr/local/bin:

fastq2fasta.py
Simple FASTQ to FASTA conversion.
fetch_phix.sh
Downloads the PhiX174 reference genome.
fetch_igblastdb.sh
Downloads the IgBLAST reference database.
fetch_imgtdb.sh
Downloads the IMGT reference database.
imgt2igblast.sh
Imports the IMGT reference database into IgBLAST.
run_igblast.sh
Simple IgBLAST wrapper for running IgBLAST with the required arguments using the IMGT reference database.

Template Pipeline Scripts

The following pipeline templates are found in /usr/local/bin:

presto-abseq
A start to finish pRESTO processing script for AbSeq data.
changeo-igblast
Performs V(D)J alignment using IgBLAST and post-processes the output into the Change-O data standard.
changeo-clone
Assigns Ig sequences into clonally related lineages and builds full germline sequences.
shazam-threshold
Performs automated detection of the clonal assignment threshold.
tigger-genotype
Infers V segment genotypes using TIgGER.
preprocess-phix
Removes PhiX reads from raw data files.

Data

/usr/local/share/germlines/imgt/IMGT.yaml
Information about the downloaded IMGT reference sequences.
/usr/local/share/germlines/imgt/<species>/vdj/
Directory containing IMGT-gapped V(D)J reference sequences in FASTA format.
/usr/local/share/igblast/
IgBLAST data directory.
/usr/local/share/igblast/fasta/
Directory containing ungapped IMGT references sequences with IGH/IGL/IGL and TRA/TRB/TRG/TRD combined into single FASTA files, respectively.
/usr/local/share/protocols
Directory containing primer, template switch and internal constant region sequences for various experimental protocols in FASTA format.