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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

  • Added reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.[bed,bim,fam] files, to simplify steps for MAGMA analysis in GSA-MiXeR protocol
  • Added reference/ldsc/1000G_EUR_Phase3_plink/baseline_v2.2_1000G.EUR.QC.@.annot.gz files - binary functional annotations based

Updated

  • Updated PLINK2.0 (20240516)
  • Added installation information to the README.md file.
  • Mambaforge for Python 3.10.14 environment (was Python 3.8)
  • Updated PLINK1.9 (20231211) and PLINK2.0 (20231211) versions (and revised corresponding syntax in mixer_simu example)
  • Updated apt package versions to current
  • Revised installer scripts
  • Updated READMEs and example files

Added

  • Building and pushing the MiXeR images in both Docker and Singularity format to the ghcr.io registry is now automated using GitHub Actions.
  • Added gdb to apt_get_essentials.sh for debugging.
  • Version pinned for Ubuntu, conda and conda packages.
  • Run conda clean -a -y in Dockerfile reducing image size.
  • Added usecases/run_mixer.ipynb Jupyter notebook for simplifying Slurm job submissions for lists of traits.
  • Include module purge in Slurm job scripts to avoid conflicts with system modules.

Changed

  • Use Ubuntu 20.04 LTS as base image for Docker and Singularity containers.
  • Rebuilt container w. md5 checksum b344119fd1f8f9c425f0edea78c08881 (commit: 3882739)

Fixed

  • Removed use of np.unique in usecases/run_mixer.ipynb
  • Fixed incorrect job dependency bug in usecases/run_mixer.ipynb
  • Updated outdated paths to comorment containers on p697
  • Explicitly named log files in Slurm .job scripts
  • Fixed reference to wrong container file in MIXER_SIMU.job

[1.3.0] - 2022-09-30

Added

  • MiXeR software v1.3.0 packaged into singularity container. MD5 checksum:

    7e233fdc91e9de1f89cb579af3809752  mixer.sif

  • Reference datasets:

    • hapgen/chr21.[bed,bim,fam] - synthetic genotypes (N=10.000 individuals) with realistic LD structure generated using hapgen2 software
    • ldsc/1000G_EUR_Phase3_plink/* - reference data, derived from 1000 genomes Phase3 data, EUR population, pre-processed for LD score regression software (https://alkesgroup.broadinstitute.org/LDSCORE/)
    • sumstats/* - several GWAS summary statistics on real phenotypes. See reference/sumstats/README.md for more information.

  • Examples of how to apply MiXeR on synthetic and real data