Using with Docker
Official MiXCR Docker repository is hosted on the GitHub along with this repo.
> docker run --rm \ -e MI_LICENSE="...license-token..." \ -v /path/to/raw/data:/raw:ro \ -v /path/to/put/results:/work \ ghcr.io/milaboratory/mixcr/mixcr:latest \ align -s hs \ /raw/data_R1.fastq.gz \ /raw/data_R2.fastq.gz \ alignments.vdjca
The docker repo provides pre-built docker images for all release versions of MiXCR starting from 1.1. Images come in two flavours: "mixcr only" (i.e tag
4.0.0) and co-bundled "mixcr + imgt reference" (i.e. tag
4.0.0-imgt), for the latter please see the license note below. All bundled versions before and including
4.0.0 contain IMGT reference version
202214-2 from here, this might be different from the images from the previous official docker registry on Docker Hub (which is now deprecated and planned for removal).
See docker packages page for the full list of tags including development builds.
Setting the license
There are several ways to pass the license for mixcr when executed inside a container:
- Using environment variable:
docker run \ -e MI_LICENSE="...license-token..." \ ....
- Using license file:
docker run \ -v /path/to/mi.license:/opt/mixcr/mi.license:ro \ ....
- If it is hard to mount
mi.licensefile into already populated folder
/opt/mixcr/(i.e. in Kubernetes or with other container orchestration tools), you can tell MiXCR where to look for it:
docker run \ -v /path/to/folder_with_mi_license:/secrets:ro \ -e MI_LICENSE_FILE="/secrets/milicense.txt" \ ....
Migration from the previous docker images
New docker images define
mixcr startup script as an entrypoint of the image, compared to the previous docker repo where
bash was used instead. So, what previously was executed this way:
docker run ... old/mixcr/image/address:with_tag mixcr align ...
now will be
docker run ... new/mixcr/image/address:with_tag align ...
For those who rely on other tools inside the image, beware, new build relies on a different base image and has slightly different layout.
mixcr startup script is added to
PATH environment variable, so even if you specify custom entrypoint, there is no need in using of full path to run
License notice for IMGT images
Data coming from IMGT server may be used for academic research only, provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)."
References to cite: Lefranc, M.-P. et al., Nucleic Acids Research, 27, 209-212 (1999) Cover of NAR; Ruiz, M. et al., Nucleic Acids Research, 28, 219-221 (2000); Lefranc, M.-P., Nucleic Acids Research, 29, 207-209 (2001); Lefranc, M.-P., Nucleic Acids Res., 31, 307-310 (2003); Lefranc, M.-P. et al., In Silico Biol., 5, 0006 (2004) [Epub], 5, 45-60 (2005); Lefranc, M.-P. et al., Nucleic Acids Res., 33, D593-D597 (2005) Full text, Lefranc, M.-P. et al., Nucleic Acids Research 2009 37(Database issue): D1006-D1012; doi:10.1093/nar/gkn838 Full text.