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 2.5.0 docker pull kleinstein/immcantation:2.5.0 # Pull the latest development build docker pull kleinstein/immcantation:devel
# Pull release version 2.5.0 IMAGE="immcantation-2.5.0.img" singularity create --size 6000 $IMAGE singularity import $IMAGE docker://kleinstein/immcantation:2.5.0
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.