Release Notes
Version 4.4.0.999: July 19, 2023
Version Updates:
igblast 1.21.0
dowser 1.1.2
Image Changes:
Updated base image to Fedora 38.
Added
RAxML-NG
(https://github.com/amkozlov/raxml-ng)
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 usesinglecell-filter
. ReplacedDefineClones.py
withscoper-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
andchangeo-igblast
.Added the
-z
argument tochangeo-10x
,changeo-igblast
, andchangeo-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 oldinternal_data
andoptional_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 theleader_vexon
subdirectory.Added
imgt2cellranger.py
script which converts the IMGT reference germline header format into the input format required bycellranger 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
, anddatabase
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 topresto-clontech
.Changed name of the console logs in
presto-clontech
topipeline-presto.log
andpipeline-presto.err
(waspipeline.log
andpipeline.err
).Added
--minseq
and--mingerm
arguments totigger-genotype
to control sequence and allele exclusion criteria.The
changeo-10x
will no longer automatically archive thedb-pass
file in thetemp_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 tochangeo-clone
to specify the distance model used for cloning.Renamed the productive filter argument from
-f
to-k
inchangeo-igblast
.Added a method option of
none
toshazam-threshold
to provide a dummy mode that simply plots the distance-to-nearest distribution without threshold detection.Added
--minseq
and--mingerm
arguments totigger-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 tochangeo-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
andchangeo-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
andbuilds 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 tochangeo-igblast
to allow optional filtering of non-productive/non-functional sequences.Added
-a
argument tochangeo-clone
to allow retention of non-productive/non-functionals sequences during cloning.Added
-v
argument totigger-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
andchangeo-clone
were not working with an unspecified output directory (-o
argument).Updated CPU core detection in
tigger-genotype
andshazam-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 toshazam-threshold
to allow specification of the mixture model distributions toshazam::findThreshold
.
Image Changes:
Set Rcpp version for R package builds to
0.12.16
(from0.12.12
).
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
) inpreprocess-phix
andchangeo-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.