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¶
Template Pipeline Scripts¶
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.