Docker Container Release Notes

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 compatability 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 libaries.
  • 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.