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 3.0.0
docker pull kleinstein/immcantation:3.0.0

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

Singularity

# Pull release version 3.0.0
IMAGE="immcantation-3.0.0.sif"
singularity build $IMAGE docker://kleinstein/immcantation:3.0.0

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 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.