Add missing packages + updates (#314)

* Add missing packages + updates
Fixes #310

* fix

* pooch

Author: espenhgn

CHANGELOG.md

@@ -37,6 +37,17 @@ Removed features goes here
 
 Miscellaneous goes here
 
+## 1.13.0 - 2025-11-27
+
+### Added
+
+* added misc. R and Python packages to respective containers
+* added script to install R backages from [MRCIEU-Universe](https://github.com/r-universe/mrcieu)
+
+### Updated 
+
+* updated PLINK2 to v2.0.0-a.6.28 (Nov. 23, 2025) across containers
+
 ## [1.12.0] - 2025-11-26
 
 ### Fixed

docker/dockerfiles/python3/Dockerfile

@@ -34,6 +34,7 @@ RUN mamba install python=3.10.6 \
     miniwdl=1.12.1 \
     miniwdl-slurm=0.2.0 \
     more-itertools=9.0.0 \
+    networkx=3.4 \
     numdifftools=0.9.39 \
     numba=0.60.0 \
     numpy=1.23.3 \
@@ -62,16 +63,21 @@ RUN mamba install python=3.10.6 \
     mamba clean -a -y
 
 # pip install stuff in env.
-RUN pip install --no-cache-dir cbgen==1.0.2 && \
-    pip install --no-cache-dir bgen-reader==4.0.8 && \
-    pip install --no-cache-dir bed-reader==0.2.24 && \
-    pip install --no-cache-dir dxpy==0.383.1 && \
-    pip install --no-cache-dir pysnptools==0.5.7 && \
-    pip install --no-cache-dir fastlmm==0.6.3 && \
-    pip install --no-cache-dir plinkio==0.9.8 && \
-    pip install --no-cache-dir LDpred==1.0.11 && \
-    pip install --no-cache-dir pycap==2.1.0 && \
-    pip install --no-cache-dir pyliftover==0.4.1 && \
+RUN pip install --no-cache-dir --no-deps cbgen==1.0.2 \
+    bgen-reader==4.0.8 \
+    bed-reader==0.2.24 \
+    dxpy==0.383.1 \
+    fastlmm==0.6.3 \
+    hdf5storage==0.2.2 \
+    LDpred==1.0.11 \
+    Pgenlib==0.93.0 \
+    plinkio==0.9.8 \
+    plinkliftover \
+    poetry==2.2.1 \
+    pooch==1.8.2 \
+    pycap==2.1.0 \
+    pyliftover==0.4.1 \
+    pysnptools==0.5.7 && \
     pip cache purge 
 
 # Plink (as python_convert depends on plink)

docker/dockerfiles/r/Dockerfile

@@ -43,6 +43,10 @@ RUN Rscript cran.R
 COPY /scripts/R/bioconductor.R .
 RUN Rscript bioconductor.R
 
+# MRCIEU packages:
+COPY /scripts/R/mrcieu.R .
+RUN Rscript mrcieu.R
+
 # GitHub distributed packages:
 COPY /scripts/R/github.R .
 RUN --mount=type=secret,id=github_pat \

docker/scripts/R/cran.R

@@ -11,9 +11,11 @@ packages <- list(
     'argparser',
     'arsenal',
     'arrow',
+    'bdsmatrix',
     'bigreadr',
     'bigsnpr',
     'BiocManager',
+    'bit',
     'bit64',
     'brant',
     'brms',
@@ -26,14 +28,17 @@ packages <- list(
     'compareC',
     'correlation',
     'corrplot',
+    'coxme',
     'CPBayes',
     'DescTools',
     'data.table',
     'dendextend',
     'dplyr',
     'EFAtools',
+    'egg',
     'fastICA',
     'fcfdr',
+    'feather',
     'flextable',
     'fmsb',
     'foreign',
@@ -43,6 +48,8 @@ packages <- list(
     'ggalluvial',
     'ggcorrplot',
     'ggplot2',
+    'ggpubr',
+    'ggrepel',
     'ggseg',
     'ggseg3d',
     'ggstar',
@@ -60,11 +67,13 @@ packages <- list(
     'ieugwasr',
     'imputeMissings',
     'jtools',
+    'kinship2',
     'lavaan',
     'lightgbm',
     'lmerTest',
     'magrittr',
     'MatrixEQTL',
+    'matrixStats',
     'MendelianRandomization',
     'mgcv',  # has gamm function
     'miniCRAN',
@@ -75,10 +84,12 @@ packages <- list(
     'optparse',
     'parameters',
     'patchwork',
+    'pgenlibr',
     'PooledCohort',
     'pracma',
     'PredictABEL',
     'pROC',
+    'psych',
     'qqman',
     'QRISK3',
     'r2redux',
@@ -95,6 +106,7 @@ packages <- list(
     'seqminer',
     'semTools',
     'simplecolors',
+    'simsalapar',
     'sp',
     'splines2',
     'stringr',

docker/scripts/R/github.R

@@ -8,27 +8,14 @@ cat("GitHub PAT length: ", nchar(auth_token), "\n")
 # GitHub packages w. Git SHA
 packages <- list(
     'alexploner/cfdr.pleio' = '76d5085e6d3f3ca9576d5d7564d2acf11bcfd021',
+    'amslala/regtools' = 'v0.2.0',
     'dajiangliu/rareGWAMA' = '72e962dae19dc07251244f6c33275ada189c2126',
     'deepchocolate/glm-extras' = 'ecba68c0378fc953edf8fe594ce914aff8ada6fa',
-    'GenomicSEM/GenomicSEM' = '8e0ef594e95885b1f734f1dfcfe668b16ada2880',
     'jamesliley/cfdr' = 'ec5fddbd27c746a470eb827dc249a80194b231e8',
     'jamesliley/cFDR-common-controls' = '9b923fea283e2373ee8effa2909620a1930004bd',
-    # gwasvcf deps:
-    'MRCIEU/genetics.binaRies' = 'b0324f180476d80c43bba2ab026b72c5be426a92',
-    'MRCIEU/gwasglue2' = 'c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa',
-    'MRCIEU/gwasvcf' = '477b365da8522e9a47f3bce51993d5f36df49ceb',
-    # gwasglue/TwoSampleMR deps:
-    'rondolab/MR-PRESSO' = '3e3c92d7eda6dce0d1d66077373ec0f7ff4f7e87',
-    'gqi/MRMix'='56afdb2bc96760842405396f5d3f02e60e305039',
-    'WSpiller/RadialMR' = '0ed91f83aebf265a09482561c128c830e58ed697',
-    'qingyuanzhao/mr.raps' = '27b96f31e26ae97a395422bd757f514a7f96cc85',
-    'MRCIEU/TwoSampleMR' = '578c68fa754c57d764553812bf85d69ecf43b011',
-    'MRCIEU/gwasglue' = 'c2d5660eed389e1a9b3e04406b88731d642243f1',
-    'noahlorinczcomi/MRBEE' = '6295549a1f5a158c6701eb793646d60c8aef11ca',
     'norment/normentR' = 'dfa1fbae9587db6c3613b0405df4f9cfa98ee0e1',
     'psychgen/phenotools' = '62dd11e111d8d952837c9f207557e9b297ba56bc',
     'wouterpeyrot/CCGWAS' = 'ce9764da946189623a0164f156ad119773bc32f5',
-    'WSpiller/MVMR' = '65705da9421b6235c7458dba6f01cddfebfe96f5',
     'xiashen/MultiABEL' = '7067fe6753c74f6580029abc82bce914472b4b16',
     'amorris28/hazrd' = 'ff9f1690e930792f29e1fd87e25c0dc8632339d5',
     'cnfoley/hyprcoloc' = '26ea5953a46b3e204dfa8eadd202f746244afa13',

docker/scripts/R/mrcieu.R

@@ -0,0 +1,33 @@
+require(devtools)
+repos <- c("https://mrcieu.r-universe.dev", "https://cloud.r-project.org")
+
+packages <- list(
+  "GenomicSEM" = "0.0.5",
+  "genetics.binaRies" = "0.1.2",
+  "gwasglue2" = "0.0.0.9000",
+  "gwasvcf" = "0.1.5",
+  "MRPRESSO" = "1.0",
+  "MRMix" = "0.1.0",
+  "RadialMR" = "1.2.1",
+  "mr.raps" = "0.4.3",
+  "TwoSampleMR" = "0.6.24",
+  "gwasglue" = "0.0.0.9001",
+  "MRBEE" = "0.1.0",
+  "MVMR" = "0.4.2")
+
+for (package in names(packages)) {
+  version <- packages[[package]]
+  cat("Installing package ", package, " from MRCIEU with version ", version, "\n")
+  tryCatch(
+  {
+    devtools::install_version(package, version=version, repos=repos)
+  },
+  error = function(e) {
+    cat("Error occurred during package installation:\n")
+    print(e)
+    quit(status=1, save="no")
+  },
+  finally = {
+  }
+ )
+}

docker/scripts/install_plink2.sh

@@ -1,7 +1,7 @@
 #!/bin/sh
 set -euo pipefail
 
-wget --no-check-certificate https://github.com/chrchang/plink-ng/releases/download/v2.0.0-a.6.23/plink2_linux_x86_64.zip && \
+wget --no-check-certificate https://github.com/chrchang/plink-ng/releases/download/v2.0.0-a.6.28/plink2_linux_x86_64.zip && \
     unzip -j plink2_linux_x86_64.zip && \
     rm -rf plink2_linux_x86_64.zip
 

docker/scripts/install_plink2_avx2.sh

@@ -1,7 +1,7 @@
 #!/bin/sh
 set -euo pipefail
 
-wget --no-check-certificate https://github.com/chrchang/plink-ng/releases/download/v2.0.0-a.6.23/plink2_linux_avx2.zip && \
+wget --no-check-certificate https://github.com/chrchang/plink-ng/releases/download/v2.0.0-a.6.28/plink2_linux_avx2.zip && \
     unzip -j plink2_linux_avx2.zip && \
     rm -rf plink2_linux_avx2.zip
 # we install non-avx plink2 so that default plink runs on any  CPU architecture

tests/extras/r.R

@@ -6,12 +6,14 @@ library(testthat)
 # List of libraries to check
 libraries_to_check <- c(
     "AER",
-    "argparser", 
-    "bigreadr", 
+    "argparser",
+    "bdsmatrix",
+    "bigreadr",
     "bigsnpr",
     "BiocGenerics",
     "BiocManager",
-    'bit64',
+    "bit",
+    "bit64",
     "caret",
     "coloc",
     "colocboost",
@@ -22,6 +24,8 @@ libraries_to_check <- c(
     "data.table",
     "dplyr",
     "EFAtools",
+    "egg",
+    "feather",
     "flextable",
     "fmsb",
     "foreign",
@@ -43,6 +47,7 @@ libraries_to_check <- c(
     "qqman",
     "rareGWAMA",
     "reghelper",
+    "regtools",
     "remotes",
     "RiskScorescvd",
     "rmarkdown",
@@ -76,6 +81,7 @@ libraries_to_check <- c(
     "clusterProfiler",
     "correlation",
     "corrplot",
+    "coxme",
     "CPBayes",
     "DBI",
     "dendextend",
@@ -88,6 +94,7 @@ libraries_to_check <- c(
     "ggalluvial",
     "ggcorrplot",
     "ggpubr",
+    "ggrepel",
     "ggseg",
     "ggseg3d",
     "ggstar",
@@ -117,8 +124,10 @@ libraries_to_check <- c(
     "lme4",
     "lmerTest",
     "lubridate",
+    "kinship2",
     "MASS",
     "MatrixEQTL",
+    "matrixStats",
     "MendelianRandomization",
     "mgcv",
     "miniCRAN",
@@ -136,6 +145,7 @@ libraries_to_check <- c(
     "org.Hs.eg.db",
     "parallel",
     "patchwork",
+    "pgenlibr",
     "phenotools",
     "pracma",
     "PredictABEL",
@@ -153,6 +163,7 @@ libraries_to_check <- c(
     "semptools",
     "semTools",
     "simplecolors",
+    "simsalapar",
     "sp",
     "splines",
     "splines2",

version/version.py

@@ -1,5 +1,5 @@
 _MAJOR = "1"
-_MINOR = "12"
+_MINOR = "13"
 # On main and in a nightly release the patch should be one ahead of the last
 # released build.
 _PATCH = "0"