Update/add software

.github/workflows/docker.yml

@@ -10,7 +10,7 @@ jobs:
       - name: Check out code
         uses: actions/checkout@v3
       - name: hadolint
-        uses: reviewdog/action-hadolint@v1
+        uses: reviewdog/action-hadolint@v1.50.5
         with:
           reporter: github-pr-review # Default is github-pr-check
           fail_on_error: true

CHANGELOG.md

@@ -37,6 +37,17 @@ Removed features goes here
 
 Miscellaneous goes here
 
+## 1.16.0 - 2026-06-08
+
+### Added
+
+* Added R packages: mirt, PerformanceAnalytics, tidymodels, splitstackshape, fastDummies, pbapply, kernlab, PheWAS
+* Added Python packages pymoo, paretoset, pyhazrd
+
+### Removed
+
+* drop KING relatedness software from gwas build, due to issues with downloading the binary and lack of updates from the developer
+
 ## 1.15.0 - 2026-02-23
 
 ### Added

docker/dockerfiles/gwas/Dockerfile

@@ -72,10 +72,10 @@ RUN bash /tmp/snptest/install_snptest.sh && \
     rm -rf /tmp/snptest
 
 # king
-WORKDIR /tmp/king
-COPY /scripts/install_king.sh /tmp/king/
-RUN bash /tmp/king/install_king.sh && \
-    rm -rf /tmp/king
+# WORKDIR /tmp/king
+# COPY /scripts/install_king.sh /tmp/king/
+# RUN bash /tmp/king/install_king.sh && \
+#     rm -rf /tmp/king
 
 # ldak
 WORKDIR /tmp/ldak

docker/dockerfiles/python3/Dockerfile

@@ -59,6 +59,7 @@ RUN mamba install python=3.12.12 \
     psycopg2=2.9.11 \
     pyarrow=22.0.0 \
     pydot=4.0.1 \
+    pymoo=0.6.1.5 \
     pymysql=1.1.2 \
     pyqt=5.15.11 \
     pyreadr=0.5.4 \
@@ -98,13 +99,16 @@ RUN pip install --no-cache-dir --no-deps \
     hdf5storage==0.2.2 \
     LDpred==1.0.11 \
     Pgenlib==0.93.0 \
+    paretoset==1.2.5 \
     plinkio==0.9.8 \
     plinkliftover==0.5.2 \
     poetry==2.2.1 \
     pooch==1.8.2 \
     pycap==2.7.0 \
     pyliftover==0.4.1 \
-    pysnptools==0.5.14 && \
+    pysnptools==0.5.14 \
+    git+https://github.com/espenhgn/hazrd.git@copilot/convert-hazrd-to-pyhazrd \
+    && \
     pip cache purge
 
 # Plink (as python_convert depends on plink)

docker/dockerfiles/r/Dockerfile

@@ -17,7 +17,7 @@ RUN apt-get update -y && apt-get install -y --no-install-recommends \
     rm -rf /var/lib/apt/lists/*
 
 RUN apt-get update -y && apt-get install -y --no-install-recommends \
-    curl=8.5.0-2ubuntu10.6 \
+    curl=8.5.0-2ubuntu10.9 \
     libperl-dev=5.38.2-3.2ubuntu0.2 \
     libgslcblas0=2.7.1+dfsg-6ubuntu2 \
     lmodern=2.005-1 \

docker/scripts/R/cran.R

@@ -1,129 +1,136 @@
 require(devtools)
 url <- "https://packagemanager.posit.co/cran/__linux__/noble/2025-08-01"
-dependencies <- c('Depends', 'Imports', 'LinkingTo')
-upgrade <- 'default'
+dependencies <- c("Depends", "Imports", "LinkingTo")
+upgrade <- "default"
 
 options(repos = c(CRAN = url))
 
 # CRAN packages w. version
 packages <- list(
-    'AER',
-    'argparser',
-    'arsenal',
-    'arrow',
-    'bdsmatrix',
-    'bigreadr',
-    'bigsnpr',
-    'BiocManager',
-    'bit',
-    'bit64',
-    'brant',
-    'brms',
-    'carat',
-    'caret',
-    'circlize',
-    'coloc',
-    'colocboost',
-    'colocPropTest',
-    'compareC',
-    'correlation',
-    'corrplot',
-    'coxme',
-    'CPBayes',
-    'DescTools',
-    'data.table',
-    'dendextend',
-    'dplyr',
-    'EFAtools',
-    'egg',
-    'fastICA',
-    'fcfdr',
-    'feather',
-    'flextable',
-    'fmsb',
-    'foreign',
-    'GCPBayes',
-    'geepack',
-    'genio',
-    'ggalluvial',
-    'ggcorrplot',
-    'ggplot2',
-    'ggpubr',
-    'ggrepel',
-    'ggseg',
-    'ggseg3d',
-    'ggstar',
-    'ggthemes',
-    'ggpubr',
-    'gitcreds',
-    'glmmTMB',
-    'glmnet',
-    'glue',
-    'gplots',
-    'gtsummary',
-    'Haplin',
-    'here',
-    'homologene',
-    'ieugwasr',
-    'imputeMissings',
-    'jtools',
-    'kinship2',
-    'lavaan',
-    'lightgbm',
-    'lmerTest',
-    'magrittr',
-    'matlab',
-    'matlab2r',
-    'MatrixEQTL',
-    'matrixStats',
-    'MendelianRandomization',
-    'mgcv',  # has gamm function
-    'miniCRAN',
-    'moments',
-    'MplusAutomation',
-    'MVN',
-    'mvtnorm',
-    'optparse',
-    'parameters',
-    'patchwork',
-    'pgenlibr',
-    'PooledCohort',
-    'pracma',
-    'PredictABEL',
-    'pROC',
-    'psych',
-    'qqman',
-    'QRISK3',
-    'r2redux',
-    'reghelper',
-    'remotes',
-    'RiskScorescvd',
-    'rjags',
-    'rmatio',
-    'R.matlab',
-    'ROCR',
-    'rmarkdown',
-    'rstan',
-    'runonce',
-    'scales',
-    'semptools',
-    'seqminer',
-    'semTools',
-    'simplecolors',
-    'simsalapar',
-    'sp',
-    'splines2',
-    'stringr',
-    'susieR',
-    'survey',
-    'survival',
-    'survminer',
-    'tibble',
-    'tidyr',
-    'tree',
-    'vctrs',
-    'xgboost',
-    'zlib')
+    "AER",
+    "BiocManager",
+    "CPBayes",
+    "DescTools",
+    "EFAtools",
+    "GCPBayes",
+    "Haplin",
+    "MVN",
+    "MatrixEQTL",
+    "MendelianRandomization",
+    "MplusAutomation",
+    "PerformanceAnalytics",
+    "PooledCohort",
+    "PredictABEL",
+    "QRISK3",
+    "R.matlab",
+    "ROCR",
+    "RiskScorescvd",
+    "argparser",
+    "arrow",
+    "arsenal",
+    "bdsmatrix",
+    "bigreadr",
+    "bigsnpr",
+    "bit",
+    "bit64",
+    "brant",
+    "brms",
+    "carat",
+    "caret",
+    "circlize",
+    "coloc",
+    "colocPropTest",
+    "colocboost",
+    "compareC",
+    "correlation",
+    "corrplot",
+    "coxme",
+    "data.table",
+    "dendextend",
+    "dplyr",
+    "egg",
+    "fastDummies",
+    "fastICA",
+    "fcfdr",
+    "feather",
+    "flextable",
+    "fmsb",
+    "foreign",
+    "geepack",
+    "genio",
+    "ggalluvial",
+    "ggcorrplot",
+    "ggplot2",
+    "ggpubr",
+    "ggpubr",
+    "ggrepel",
+    "ggseg",
+    "ggseg3d",
+    "ggstar",
+    "ggthemes",
+    "gitcreds",
+    "glmmTMB",
+    "glmnet",
+    "glue",
+    "gplots",
+    "gtsummary",
+    "here",
+    "homologene",
+    "ieugwasr",
+    "imputeMissings",
+    "jtools",
+    "kernlab",
+    "kinship2",
+    "lavaan",
+    "lightgbm",
+    "lmerTest",
+    "magrittr",
+    "matlab",
+    "matlab2r",
+    "matrixStats",
+    "mgcv",
+    "miniCRAN",
+    "mirt",
+    "moments",
+    "mvtnorm",
+    "optparse",
+    "pbapply",
+    "pROC",
+    "parameters",
+    "patchwork",
+    "pgenlibr",
+    "pracma",
+    "psych",
+    "qqman",
+    "r2redux",
+    "reghelper",
+    "remotes",
+    "rjags",
+    "rmarkdown",
+    "rmatio",
+    "rstan",
+    "runonce",
+    "scales",
+    "semTools",
+    "semptools",
+    "seqminer",
+    "simplecolors",
+    "simsalapar",
+    "sp",
+    "splines2",
+    "splitstackshape",
+    "stringr",
+    "survey",
+    "survival",
+    "survminer",
+    "susieR",
+    "tibble",
+    "tidymodels",
+    "tidyr",
+    "tree",
+    "vctrs",
+    "xgboost",
+    "zlib")
 
 
 # install package from CRAN and quit with error if installation fails
@@ -138,7 +145,7 @@ for (package in packages) {
     error = function(e) {
         cat("Error occurred during package installation:\n")
         print(e)
-        quit(status=1, save='no')
+        quit(status=1, save="no")
     },
     finally = {
     }

docker/scripts/R/github.R

@@ -33,15 +33,17 @@ packages <- list(
     "wouterpeyrot/CCGWAS" = "ce9764da946189623a0164f156ad119773bc32f5",
     "WSpiller/MVMR" = "65705da9421b6235c7458dba6f01cddfebfe96f5",
     "xiashen/MultiABEL" = "7067fe6753c74f6580029abc82bce914472b4b16",
-    "amorris28/hazrd" = "ff9f1690e930792f29e1fd87e25c0dc8632339d5",
+    "amorris28/hazrd" = "c75b2f12361d98f4c50841ec67190e9e7b14c322",
     "cnfoley/hyprcoloc" = "26ea5953a46b3e204dfa8eadd202f746244afa13",
     "zhenin/HDL/HDL" = "551a8864c5ed3389a6892743ff059357735dc195",
     "JBPG/Gsens" = "6cac02ba1ccaf38870e2526076f0306c0cf0dc0a",
     "MRCIEU/genetics.binaRies" = "2fcd3ee3088b729c7eb34cf2aac9dc2e04fe4412",
     "mrcieu/gwasglue2" = "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa",
     "gqi/MRMix" = "56afdb2bc96760842405396f5d3f02e60e305039",
     "JianYang-Lab/gsmr2" = "e7953cc136ad1cfae14674facde21e90caddea5f",
-    "n-mounier/MRlap" = "660f026864f8bfbbad5a8206bdff7d58f5d5d05b")
+    "n-mounier/MRlap" = "660f026864f8bfbbad5a8206bdff7d58f5d5d05b",
+    "PheWAS/PheWAS" = "55dd1c24e228851922400cfba8d7db474565ccc7")
+
 
 # install package from GitHub and quit with error if installation fails
 for (package in names(packages)) {

docker/scripts/apt_get_essential.sh

@@ -12,14 +12,14 @@ apt-get update && apt-get install -y --no-install-recommends \
    build-essential=12.10ubuntu1 \
    bzip2=1.0.8-5.1build0.1 \
    cmake=3.28.3-1build7 \
-   curl=8.5.0-2ubuntu10.6 \
+   curl=8.5.0-2ubuntu10.9 \
    dos2unix=7.5.1-1 \
    gdb=15.0.50.20240403-0ubuntu1 \
    gfortran=4:13.2.0-7ubuntu1 \
    git=1:2.43.0-1ubuntu7.3 \
    less=590-2ubuntu2.1 \
    libatlas-base-dev=3.10.3-13ubuntu1 \
-   libcurl4-openssl-dev=8.5.0-2ubuntu10.6 \
+   libcurl4-openssl-dev=8.5.0-2ubuntu10.9 \
    libgomp1=14.2.0-4ubuntu2~24.04.1 \
    libgsl-dev=2.7.1+dfsg-6ubuntu2 \
    libnss3=2:3.98-1build1 \
@@ -34,7 +34,7 @@ apt-get update && apt-get install -y --no-install-recommends \
    tar=1.35+dfsg-3build1 \
    tofrodos=1.7.13+ds-6 \
    unzip=6.0-28ubuntu4.1 \
-   vim=2:9.1.0016-1ubuntu7.9 \
+   vim=2:9.1.0016-1ubuntu7.14 \
    wget=1.21.4-1ubuntu4.1 \
    zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1
 

docker/scripts/install_bcftools.sh

@@ -3,7 +3,7 @@ set -euo pipefail
 
 # deps 
 apt-get update && apt-get install -y --no-install-recommends \
-    libcurl4-gnutls-dev=8.5.0-2ubuntu10.6 \
+    libcurl4-gnutls-dev=8.5.0-2ubuntu10.9 \
     libperl-dev=5.38.2-3.2ubuntu0.2
 
 apt-get clean && \