Docker Container Installation and Overview¶
We have provided a complete installation of the Immcantation framework, its dependencies, accessory scripts, and IgBLAST in a Docker image. 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:
Images are versioned through tags with images containing official releases
denoted by meta-version numbers (
devel tag denotes the
latest development (unstabled) builds.
Getting the Container¶
Requires an installation of Docker 1.9+ or Singularity 2.3+.
# Pull release version 4.4.0 docker pull immcantation/suite:4.4.0 # 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).
# Pull release version 4.4.0 IMAGE="immcantation_suite-4.4.0.sif" singularity build $IMAGE docker://immcantation/suite:4.4.0
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¶
Template Pipeline Scripts¶
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
The following accessory scripts are found in
Simple FASTQ to FASTA conversion.
Downloads the PhiX174 reference genome.
Downloads the IgBLAST reference database.
Downloads the IMGT reference database.
Imports the IMGT reference database into IgBLAST.
Converts the IMGT fasta germline reference files to the input required by cellranger-mkvdjref.
Information about the downloaded IMGT reference sequences.
Directory containing IMGT-gapped V(D)J reference sequences in FASTA format.
IgBLAST data directory.
Directory containing ungapped IMGT references sequences with IGH/IGL/IGL and TRA/TRB/TRG/TRD combined into single FASTA files, respectively.
Directory containing primer, template switch and internal constant region sequences for various experimental protocols in FASTA format.