Docker Container Installation and Overview

We have provided a complete installation of the Immcantation framework, its dependencies, accessory scripts, and IgBLAST in a Docker container. The container also includes both the IgBLAST and IMGT reference germline sets, as well as several template pipeline scripts.

We currently have four containers available on DockerHub:

Name	Contents
immcantation/suite	Immcantation suite, supporting applications and databases.
immcantation/lab	Immcantation tutorial materials. Only for training, not to be used in production.
immcantation/base	Base image for Immcantation development builds.
immcantation/test	Immcantation unit test image.

For tutorial purposes, use immcantation/lab (be sure to replace suite with lab in the following code chunks) and follow the directions here. For all Immcantation uses, use immcantation/suite. Note that containers are versioned through tags with containers containing official releases denoted by meta-version numbers (x.y.z). The devel tag denotes the latest development (unstable) builds.

Getting the /suite Container

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

Docker

# Pull release version devel
docker pull immcantation/suite:devel

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

Our containers are Linux-based, so if you are using a Windows computer, please make sure that you are using Linux containers and not Windows containers (this can be changed in Docker Desktop and won’t affect your existing containers).

Singularity

# Pull release version devel
IMAGE="immcantation_suite-devel.sif"
singularity build $IMAGE docker://immcantation/suite:devel

The instructions to use containers from Docker Hub with Singularity can be slightly different for different versions of Singularity. If the command shown above doesn’t work for you, please visit Singularity Documentation and look for the specific command for your Singularity version under Build a container.

What’s in the /suite Container

Immcantation Tools

• pRESTO

• Change-O

• Alakazam

• SHazaM

• TIgGER

• SCOPer

• dowser

• RDI

• prestoR

Third Party Tools

• muscle

• vsearch

• CD-HIT

• BLAST

• IgBLAST

• IgPhyML

• PHYLIP

• tbl2asn

Template Pipeline Scripts

• PhiX cleaning pipeline

• NEBNext / AbSeq immune sequencing kit preprocessing pipeline

• Takara Bio / Clontech SMARTer v1 immune sequencing kit preprocessing pipeline

• Takara Bio / Clontech SMARTer v2 (UMI) immune sequencing kit preprocessing pipeline

• 10x Genomics V(D)J annotation pipeline

• IgBLAST annotation pipeline

• Clonal assignment pipeline

• Clonal threshold inference pipeline

• Genotyping pipeline

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.

imgt2cellranger.py

Converts the IMGT fasta germline reference files to the input required by cellranger-mkvdjref.

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/IGK/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.