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:
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 3.0.0 docker pull kleinstein/immcantation:3.0.0 # Pull the latest development build docker pull kleinstein/immcantation:devel
# 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¶
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.
- 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
- A start to finish pRESTO processing script for AbSeq data.
- Performs V(D)J alignment using IgBLAST and post-processes the output into the Change-O data standard.
- Assigns Ig sequences into clonally related lineages and builds full germline sequences.
- Performs automated detection of the clonal assignment threshold.
- Infers V segment genotypes using TIgGER.
- Removes PhiX reads from raw data files.
- 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.