Release Notes

Version 4.4.0.999: July 19, 2023

Version Updates:

  • igblast 1.21.0

  • dowser 1.1.2

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.