Release Notes

Version 4.7.0: January 21, 2026

Image Changes:

  • Updated base image to Fedora 42

  • Pinned ggplot2 version to 3.4.2 and xfun version to 0.55 to meet r requirements from enchantR.

  • Installed the python package receptor-utils 0.0.63

Version Updates:

  • airr 1.6.0

  • alakazam 1.4.2

  • blast 2.17.0

  • changeo 1.3.4

  • dowser 2.4.1

  • enchantr 0.1.24

  • presto 0.7.7

  • seurat 5.4.0

  • shazam 1.3.1

  • scoper 1.4.0

Version 4.6.0: April 7, 2025

Image Changes:

  • Updated base image to Fedora 41. In FC40, wget was replaced with wget2 (release notes (https://fedoraproject.org/wiki/Releases/40/ChangeSet#Wget2_as_wget)). The new wget has a few different options, and it doesn’t support ftp. If you are using custom scripts that make calls to wget in the container, and they start failing due to wget issues, most likely you need to update your script to use the right options.

  • Immcantation has moved to GitHub. The source code repositories for pRESTO, Change-O, Alakazam, SHazaM, TIgGER, SCOPer, Dowser, IgPhyML, enchantR, prestoR and the Immcantation portal are now available under https://github.com/immcantation.

Version Updates:

  • dowser 2.3.0

  • changeo 1.3.1

  • presto 0.7.4

  • airr_py 1.5.1

  • blast 2.16.0

  • raxml 1.2.2

  • seurat 5.2.1

  • vsearch 2.30.0

Version 4.5.0: January 25, 2024

Version Updates:

  • presto 0.7.2

  • alakazam 1.3.0

  • shazam 1.2.0

  • tigger 1.1.0

  • scoper 1.3.0

  • dowser 2.1.0

  • enchantr 0.1.10

  • rabhit 0.2.5

  • igblast 1.22.0

  • seurat 5.0.1

Image Changes:

Version 4.4.0: December 15, 2022

Version Updates:

  • presto 0.7.1

  • changeo 1.3.0

  • alakazam 1.2.1

  • shazam 1.1.2

  • tigger 1.0.1

  • scoper 1.2.1

  • dowser 1.1.1

  • prestor 0.0.8

  • blast 2.13.0

  • igblast 1.20.0

  • igphyml 1.1.5

  • airr-py 1.4.1

  • airr-r 1.4.1

Image Changes:

  • Updated base image to Fedora 37.

  • Added the Seurat R package (version 4.3.0).

  • Added build of constant region databases to imgt2igblast.sh.

Pipeline Changes:

  • Added the scoper-clone pipeline to perform clonal clustering using the SCOPer package.

  • Added the singlecell-filter pipeline to remove cells with with zero or more than one heavy chain sequences.

  • Updated changeo-10x. Added a new step to use singlecell-filter. Replaced DefineClones.py with scoper-clone.

Version 4.3.0: November 8, 2021

Version Updates:

  • presto 0.7.0

  • changeo 1.2.0

  • alakazam 1.2.0

  • shazam 1.1.0

  • scoper 1.2.0

  • dowser 0.1.0

  • prestor 0.0.7

Pipeline Changes:

  • Added the presto-clontech-umi pipeline to preprocess data from the Takara Bio / Clontech SMARTer v2 kit that includes UMIs.

Version 4.2.0: June 21, 2021

Version Updates:

  • presto 0.6.2

  • changeo 1.1.0

  • alakazam 1.1.0

  • airr-py 1.3.1

  • igblast 1.17.1

Pipeline Changes:

  • Added support for rat, rabbit and rhesus macaque to changeo-10x and changeo-igblast.

  • Added the -z argument to changeo-10x, changeo-igblast, and changeo-clone to allow compression and cleaning of temporary intermediate files to be disabled.

  • Updated changeo-igblast to use the new IgBLAST wrapper in changeo (AssignGenes).

Image Changes:

  • Updated base image to Fedora 33.

  • Fixed a Biopython v1.77 incompatibility in fastq2fasta.py.

  • Updated fetch_igblastdb.sh for new file locations and disabled download of old internal_data and optional_file directories by default.

  • Added support for rat, rabbit and rhesus macaque to fetch_imgtdb.sh.

  • Added download of artificially spliced V exon and leader sequences to fetch_imgtdb.sh. Sequences are downloaded into the leader_vexon subdirectory.

  • Added imgt2cellranger.py script which converts the IMGT reference germline header format into the input format required by cellranger mkvdjref.

Version 4.1.0: August 12, 2020

Version Updates:

  • presto 0.6.1

  • alakazam 1.0.2

  • shazam 1.0.2

  • scoper 1.1.0

  • rabhit 0.1.5

Pipeline Changes:

  • Fixed a clonal clustering threshold detection warning causing early exit of changeo-10x in some cases.

Image Changes:

  • Fixed a Biopython v1.77 incompatibility in clean_imgtdb.py.

  • Updated IgBLAST installation procedure for new structure of internal_data, optional_file, and database directories.

Version 4.0.0: June 1, 2020

General:

  • License changed to AGPL-3 for scripts, core packages, and other software code. Non-software content remains unchanged under the CC BY-SA 4.0 license.

  • Updated base image to Fedora 31.

Version Updates:

  • presto 0.6.0

  • changeo 1.0.0

  • alakazam 1.0.1

  • shazam 1.0.0

  • tigger 1.0.0

  • scoper 1.0.1

  • prestor 0.0.6

  • igphyml 1.1.3

  • igblast 1.16.0

  • airr-py 1.3.0

  • airr-r 1.3.0

Pipeline Changes:

  • Changed the default output format of all pipeline scripts to the AIRR Rearrangement standard. The legacy Change-O format is still supported by specifying -f changeo.

  • Added report generation and the -y argument specifying the report yaml config file to presto-clontech.

  • Changed name of the console logs in presto-clontech to pipeline-presto.log and pipeline-presto.err (was pipeline.log and pipeline.err).

  • Added --minseq and --mingerm arguments to tigger-genotype to control sequence and allele exclusion criteria.

  • The changeo-10x will no longer automatically archive the db-pass file in the temp_files.tar.gz tarball.

Version 3.1.0: December 16, 2019

Version Updates:

  • shazam 0.2.2

Version 3.0.0: August 29, 2019

Version Updates:

  • alakazam 0.3.0

  • presto 0.5.13

  • scoper 0.2.0

  • shazam 0.2.1

  • tigger 0.4.0

  • igphyml 1.0.6

  • igblast 1.14.0

  • blast 2.9.0

  • vsearch 2.13.6

  • cd-hit 4.8.1

Pipeline Changes:

  • Added the -f argument to multiple pipelines to toggle output between the Change-O standard (changeo) and the AIRR Rearrangement standard (airr).

  • Added the -m argument to changeo-clone to specify the distance model used for cloning.

  • Renamed the productive filter argument from -f to -k in changeo-igblast.

  • Added a method option of none to shazam-threshold to provide a dummy mode that simply plots the distance-to-nearest distribution without threshold detection.

  • Added --minseq and --mingerm arguments to tigger-genotype to allow specification of novel allele detection cutoffs.

Image Changes:

  • Added the RAbHIT R package.

  • Added the changeo-10x pipeline to process 10X Genomics V(D)J data.

  • Added the presto-clontech pipeline to preprocess data from the Takara Bio / Clontech SMARTer kit.

  • Added some universal C-region reference sequences to /usr/local/share/protocols.

  • Added the pipelines report command to show a description of available pipeline commands.

  • Fixed a dependency version issue that prevented tbl2asn from running.

  • Fixed Mac OS compatibility in fetch_imgtdb.

Version 2.7.0: February 1, 2019

Version Updates:

  • presto 0.5.11

  • changeo 0.4.5

  • shazam 0.1.11

  • blast 2.8.1

Version 2.6.0: December 9, 2018

Version Updates:

  • igblast 1.12.0

Pipeline Changes:

  • Added -i argument to changeo-igblast to allow retention of partial alignments.

Image Changes:

  • Base system changed to Fedora 29.

  • Moved setup of R package build environment to base image.

Version 2.5.0: November 1, 2018

Version Updates:

  • igblast 1.11.0

  • muscle 3.8.425

  • vsearch 2.9.1

Image Changes:

  • Added error checking to versions report command.

Version 2.4.0: October 27, 2018

Version Updates:

  • changeo 0.4.4

Version 2.3.0: October 21, 2018

Version Updates:

  • presto 0.5.10

  • changeo 0.4.3

  • tigger 0.3.1

Image Changes:

  • Added scoper R package.

  • Added IgPhyML.

  • Removed strict Rcpp version requirement (was fixed at 0.12.16).

  • Added libGL and libGLU to base image.

Version 2.2.0: October 5, 2018

Version Updates:

  • tigger 0.3.0

  • airr python library 1.2.1

Pipeline Changes:

  • Fixed compression error messages in changeo-igblast and changeo-clone.

  • Removed support for tigger versions below 0.3.0 from tigger-genotype.

Image Changes:

  • Adjusted version/changeset detection and output in the versions report and builds report commands.

Version 2.1.0: September 20, 2018

Version Updates:

  • alakazam 0.2.11

  • shazam 0.1.10

  • prestor 0.0.5

  • vsearch 2.8.4

  • BLAST 2.7.1

  • IgBLAST 1.10.0

Pipeline Changes:

  • Subsampling is no longer performed by default in shazam-threshold.

Version 2.0.0: September 8, 2018

Version Updates:

  • pRESTO 0.5.9

  • Change-O 0.4.2

  • airr 1.2.0

Image Changes:

  • Added tbl2asn.

Pipeline Changes:

  • Changed behavior of subsampling argument to shazam-threshold to subsample distances after nearest-neighbor distance calculation rather than rows before distance calculation.

Version 1.10.2: July 3, 2018

Pipeline Changes:

  • Added data set subsampling to shazam-threshold with a default value of 15000 records.

  • Added -f argument to changeo-igblast to allow optional filtering of non-productive/non-functional sequences.

  • Added -a argument to changeo-clone to allow retention of non-productive/non-functionals sequences during cloning.

  • Added -v argument to tigger-genotype to allow specification of the V genotyped column name.

Version 1.10.1: July 1, 2018

Pipeline Changes:

  • Fixed a bug wherein changeo-igblast and changeo-clone were not working with an unspecified output directory (-o argument).

  • Updated CPU core detection in tigger-genotype and shazam-threshold for compatibility with new R package versions.

Accessory Script Changes:

  • Fixed fetch_imgtdb.sh creating empty mouse IGKC and IGLC files.

Image Changes:

  • Changed default CRAN mirror setting.

Version 1.10.0: May 23, 2018

Version Updates:

  • IgBLAST 1.9.0

Pipeline Changes:

  • Changed the default threshold detection method in shazam-threshold to the smoothed density estimate with subsampling to 15000 sequences.

  • Fixed a bug wherein changeo-igblast was not reading the -b argument.

Image Changes:

  • Added RDI R package.

  • Added CD-HIT.

  • Added AIRR python and R reference libraries.

  • Added git, BLAS, and LAPACK to base image.

Version 1.9.0: April 22, 2018

Version Updates:

  • alakazam 0.2.10

  • shazam 0.1.9

Pipeline Changes:

  • Added -l <model> argument to shazam-threshold to allow specification of the mixture model distributions to shazam::findThreshold.

Image Changes:

  • Set Rcpp version for R package builds to 0.12.16 (from 0.12.12).

Version 1.8.0: March 22, 2018

Version Updates:

  • alakazam 0.2.9

  • changeo 0.3.12

  • presto 0.5.7

Pipeline Changes:

  • Removed an intermediate file and the ParseHeaders-rename step in presto-abseq.

  • Modifed tigger-genotype to work with upcoming release of tigger v0.2.12.

  • Fixed parsing of output directory argument (-o) in preprocess-phix and changeo-clone.

Image Changes:

  • Added sudo access for the magus (default) user.

Version 1.7.0: February 6, 2018

Version Updates:

  • changeo 0.3.11

Version 1.6.0: January 29, 2018

Version Updates:

  • prestor 0.0.4

Version 1.5.0: January 17, 2018

Version Updates:

  • presto 0.5.6

Version 1.4.0: December 29, 2017

Version Updates:

  • presto 0.5.5

  • phylip 3.697

Pipeline Changes:

  • Fixed a bug in presto-abseq preventing relative file paths from working with the -r argument.

  • changeo-igblast no longer terminates upon IgBLAST warnings.

Accessory Script Changes:

  • Fixed an output directory bug in fastq2fasta.py.

Image Changes:

  • Added Stern, Yaari and Vander Heiden, et al 2014 primer sets.

Version 1.3.0: October 17, 2017

Version Updates:

  • changeo 0.3.9

Pipeline Changes:

  • Fixed a bug in presto-abseq preventing relative file paths from working with the -r argument.

Version 1.2.0: October 05, 2017

Version Updates:

  • changeo 0.3.8

Version 1.1.0: September 22, 2017

Version Updates:

  • alakazam 0.2.8

  • tigger 0.2.11

  • prestor 0.0.3

Image Changes:

  • Added preprocess-phix script that removes PhiX reads.

  • Added fetch_phix.sh script that downloads the PhiX174 genome.

  • Added builds script to record and report image build date and package changesets.

  • Added -x <coordinate system> argument to presto-abseq.

  • Forced install of Rcpp to be fixed at version 0.12.12.

  • Added /oasis mount point

Version 1.0.0: August 08, 2017

  • Initial meta-versioned image.