Containerize tools (#306) and update base OS to Ubuntu 24.04LTS

* Containerize tools
Fixes #304

* fix build issues

* zlibbioc out; zlib&mr.raps in

* Containerize tools
Fixes #304

* fix some remaining build issues, prep release

* rserver instructions

* rserver info

* use static builds for shapeit5

* fix

* bump plink version

Author: espenhgn

CHANGELOG.md

@@ -37,6 +37,20 @@ Removed features goes here
 
 Miscellaneous goes here
 
+## [1.10.0] - 2025-08-27
+
+### Updated
+
+* Use Ubuntu 24.04LTS as base image for all container builds for futureproofing/security
+* Add 'paramiko' package to `python3.sif` container, updated genomicSEM and added arrow, zlib, mr.raps in `r.sif` container
+* More recent posit/cran(@2025-08-01)/bioconductor (3.19->3.22@2025-08-01) packages, removing deprecated packages (zlibbioc)
+* revised a bunch of tool installer scripts
+* shapeit5 binaries now use static builds provided by developer
+
+### Removed
+
+* temporarily remove build of qctool from gwas.sif due to GCC >= 13 issues
+
 ## [1.9.1] - 2025-03-27
 
 ### Added

docker/dockerfiles/gwas/Dockerfile

@@ -1,5 +1,5 @@
 # gwas container
-FROM ubuntu:20.04
+FROM ubuntu:24.04
 
 ENV TZ=Europe
 ENV DEBIAN_FRONTEND=noninteractive
@@ -60,10 +60,10 @@ RUN bash /tmp/gctb/install_gctb.sh && \
     rm -rf /tmp/gctb
 
 # qctool
-WORKDIR /tmp/qctool
-COPY /scripts/install_qctools.sh /tmp/qctool/
-RUN bash /tmp/qctool/install_qctools.sh && \
-    rm -rf /tmp/qctool
+# WORKDIR /tmp/qctool
+# COPY /scripts/install_qctools.sh /tmp/qctool/
+# RUN bash /tmp/qctool/install_qctools.sh && \
+#     rm -rf /tmp/qctool
 
 # snptest
 WORKDIR /tmp/snptest
@@ -146,14 +146,17 @@ COPY /scripts/patches/shapeit4.makefile.diff /tmp/shapeit4/
 RUN bash /tmp/shapeit4/install_shapeit4.sh && \
     rm -rf /tmp/shapeit4
 
-# shapeit5
+# shapeit5 - for now, use the static binaries.
 WORKDIR /tmp/shapeit5
-COPY /scripts/install_shapeit5.sh /tmp/shapeit5/
-COPY /scripts/patches/shapeit5.diff /tmp/shapeit5/
-COPY /scripts/patches/xcftools.diff /tmp/shapeit5/
-RUN bash /tmp/shapeit5/install_shapeit5.sh && \
+# COPY /scripts/install_shapeit5.sh /tmp/shapeit5/
+# COPY /scripts/patches/shapeit5.diff /tmp/shapeit5/
+# COPY /scripts/patches/xcftools.diff /tmp/shapeit5/
+# RUN bash /tmp/shapeit5/install_shapeit5.sh && \
+COPY /scripts/install_shapeit5_static.sh /tmp/shapeit5/
+RUN bash /tmp/shapeit5/install_shapeit5_static.sh && \
     rm -rf /tmp/shapeit5
 
+
 # eagle
 WORKDIR /tmp/eagle
 COPY /scripts/patches/eagle.diff /tmp/eagle/

docker/dockerfiles/hello/Dockerfile

@@ -1,5 +1,5 @@
 # demo container
-FROM ubuntu:20.04
+FROM ubuntu:24.04
 
 ENV TZ=Europe
 ENV DEBIAN_FRONTEND=noninteractive

docker/dockerfiles/python3/Dockerfile

@@ -1,5 +1,5 @@
 # gwas container
-FROM ubuntu:20.04
+FROM ubuntu:24.04
 
 ENV TZ=Europe
 ENV DEBIAN_FRONTEND=noninteractive
@@ -40,6 +40,7 @@ RUN mamba install python=3.10.6 \
     openpyxl=3.1.5 \
     pandas=2.2.3 \
     pandas-plink=2.2.9 \
+    paramiko \
     psutil=5.9.3 \
     pyarrow=19.0.1 \
     pydot=3.0.4 \

docker/dockerfiles/r/Dockerfile

@@ -1,6 +1,6 @@
 # R container
-FROM ghcr.io/rocker-org/verse:4.4.1
-# based on Ubuntu 22.04.5 LTS (jammy)
+FROM ghcr.io/rocker-org/verse:4.5.1
+# based on Ubuntu 24.04 LTS (noble)
 
 ENV TZ=Europe
 ENV DEBIAN_FRONTEND=noninteractive
@@ -10,19 +10,19 @@ WORKDIR /tmp
 
 # deps for R packages; 
 RUN apt-get update -y && apt-get install -y --no-install-recommends \
-    apt-utils=2.4.13 \
-    ca-certificates=20240203~22.04.1 && \
+    apt-utils=2.8.3 \
+    ca-certificates=20240203 && \
     update-ca-certificates && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
 RUN apt-get update -y && apt-get install -y --no-install-recommends \
-    curl=7.81.0-1ubuntu1.18 \
-    libperl-dev=5.34.0-3ubuntu1.3 \
-    libgslcblas0=2.7.1+dfsg-3 \
-    lmodern=2.004.5-6.1 \
-    texlive-latex-extra=2021.20220204-1 && \
-    wget=1.21.2-2ubuntu1.1 \
+    curl=8.5.0-2ubuntu10.6 \
+    libperl-dev=5.38.2-3.2ubuntu0.2 \
+    libgslcblas0=2.7.1+dfsg-6ubuntu2 \
+    lmodern=2.005-1 \
+    texlive-latex-extra=2023.20240207-1 && \
+    wget=1.21.4-1ubuntu4.1 \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
@@ -35,7 +35,7 @@ RUN bash /tmp/gcta/install_gcta.sh && \
 # R packages.
 # CRAN packages
 WORKDIR /tmp/
-RUN R -e "install.packages('devtools', repos='https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-04', dependencies=c('Depends', 'Imports', 'LinkingTo'))"
+RUN R -e "install.packages('devtools', repos='https://packagemanager.posit.co/cran/__linux__/noble/2025-08-01', dependencies=c('Depends', 'Imports', 'LinkingTo'))"
 COPY /scripts/R/cran.R .
 RUN Rscript cran.R
 

docker/scripts/R/bioconductor.R

@@ -2,13 +2,13 @@
 dependencies <- c('Depends', 'Imports', 'LinkingTo')
 upgrade <- 'default'
 
-url = "https://packagemanager.posit.co/bioconductor/__linux__/jammy/2024-09-04"
+url = "https://packagemanager.posit.co/bioconductor/__linux__/noble/2025-08-01"
 # Configure BioCManager to use Posit Package Manager:
-options(BioC_mirror = "https://packagemanager.posit.co/bioconductor/2024-09-04")
-options(BIOCONDUCTOR_CONFIG_FILE = "https://packagemanager.posit.co/bioconductor/2024-09-04/config.yaml")
+options(BioC_mirror = "https://packagemanager.posit.co/bioconductor/2025-08-01")
+options(BIOCONDUCTOR_CONFIG_FILE = "https://packagemanager.posit.co/bioconductor/2025-08-01/config.yaml")
 
 # Configure a CRAN snapshot compatible with Bioconductor 3.19:
-options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-04"))
+options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/noble/2025-08-01"))
 
 # Bioconductor packages
 packages <- c(
@@ -18,24 +18,24 @@ packages <- c(
     'biomaRt',
     'biomartr',
     'clusterProfiler',
+    'GenomeInfoDb',
     'gwasurvivr',
     'GWASTools',
     'limma',
     'org.Hs.eg.db',
     'rtracklayer',
     'snpStats', 
     'TMixClust',
-    'VariantAnnotation',
-    'zlibbioc')
+    'VariantAnnotation')
 
 # install package from Bioconductor and quit with error if installation fails
 library(devtools)
-BiocManager::install(version='3.19', ask=FALSE)
+BiocManager::install(version='3.22', ask=FALSE)
 
 for (package in packages) {
     tryCatch(
     {
-        BiocManager::install(package, version='3.19')
+        BiocManager::install(package, version='3.22')
     },
     error = function(e) {
         cat("Error occurred during package installation:\n")

docker/scripts/R/cran.R

@@ -1,5 +1,5 @@
 require(devtools)
-url <- "https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-04"
+url <- "https://packagemanager.posit.co/cran/__linux__/noble/2025-08-01"
 dependencies <- c('Depends', 'Imports', 'LinkingTo')
 upgrade <- 'default'
 
@@ -10,6 +10,7 @@ packages <- list(
     'AER',
     'argparser',
     'arsenal',
+    'arrow',
     'bigreadr',
     'bigsnpr',
     'BiocManager',
@@ -98,7 +99,8 @@ packages <- list(
     'tidyr',
     'tree',
     'vctrs',
-    'xgboost')
+    'xgboost',
+    'zlib')
 
 # install package from CRAN and quit with error if installation fails
 # for (package in names(packages)) {

docker/scripts/R/github.R

@@ -1,4 +1,4 @@
-url <- "https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-04"
+url <- "https://packagemanager.posit.co/cran/__linux__/noble/2025-08-01"
 dependencies <- c('Depends', 'Imports', 'LinkingTo')
 # upgrade <- 'default'
 upgrade <- 'never'
@@ -10,7 +10,7 @@ packages <- list(
     'alexploner/cfdr.pleio' = '76d5085e6d3f3ca9576d5d7564d2acf11bcfd021',
     'dajiangliu/rareGWAMA' = '72e962dae19dc07251244f6c33275ada189c2126',
     'deepchocolate/glm-extras' = 'ecba68c0378fc953edf8fe594ce914aff8ada6fa',
-    'GenomicSEM/GenomicSEM' = '199d16f5e45c040a25ee0c885338ebd667277135',
+    'GenomicSEM/GenomicSEM' = '8e0ef594e95885b1f734f1dfcfe668b16ada2880',
     'jamesliley/cfdr' = 'ec5fddbd27c746a470eb827dc249a80194b231e8',
     'jamesliley/cFDR-common-controls' = '9b923fea283e2373ee8effa2909620a1930004bd',
     # gwasvcf deps:
@@ -21,6 +21,7 @@ packages <- list(
     'rondolab/MR-PRESSO' = '3e3c92d7eda6dce0d1d66077373ec0f7ff4f7e87',
     'gqi/MRMix'='56afdb2bc96760842405396f5d3f02e60e305039',
     'WSpiller/RadialMR' = '0ed91f83aebf265a09482561c128c830e58ed697',
+    'qingyuanzhao/mr.raps' = '27b96f31e26ae97a395422bd757f514a7f96cc85',
     'MRCIEU/TwoSampleMR' = '578c68fa754c57d764553812bf85d69ecf43b011',
     'MRCIEU/gwasglue' = 'c2d5660eed389e1a9b3e04406b88731d642243f1',
     'noahlorinczcomi/MRBEE' = '6295549a1f5a158c6701eb793646d60c8aef11ca',

docker/scripts/apt_get_essential.sh

@@ -1,44 +1,43 @@
 #!/bin/sh
 set -euo pipefail
 
-apt-get update && apt-get install -y --no-install-recommends apt-utils=2.0.10
-apt-get update && apt-get install -y --no-install-recommends ca-certificates=20240203~20.04.1 && \
+apt-get update && apt-get install -y --no-install-recommends apt-utils=2.8.3
+apt-get update && apt-get install -y --no-install-recommends ca-certificates=20240203 && \
    update-ca-certificates
 
 # (!) Keep the list below sorted (!)
 apt-get update && apt-get install -y --no-install-recommends \
-   autoconf=2.69-11.1 \
-   automake=1:1.16.1-4ubuntu6 \
-   build-essential=12.8ubuntu1 \
-   bzip2=1.0.8-2 \
-   cmake=3.16.3-1ubuntu1.20.04.1 \
-   curl=7.68.0-1ubuntu2.25 \
-   dos2unix=7.4.0-2 \
-   gdb=9.1-0ubuntu1 \
-   gfortran=4:9.3.0-1ubuntu2 \
-   git=1:2.25.1-1ubuntu3.14 \
-   less=551-1ubuntu0.3 \
-   libatlas-base-dev=3.10.3-8ubuntu7 \
-   libcurl4-openssl-dev=7.68.0-1ubuntu2.25 \
-   libgomp1=10.5.0-1ubuntu1~20.04 \
-   libgsl-dev=2.5+dfsg-6+deb10u1build0.20.04.1 \
-   libnss3=2:3.98-0ubuntu0.20.04.2 \
-   libpcre2-dev=10.34-7ubuntu0.1 \
-   libxt-dev=1:1.1.5-1 \
-   pandoc=2.5-3build2 \
-   pandoc-citeproc=0.15.0.1-1build4 \
-   parallel=20161222-1.1 \
-   perl=5.30.0-9ubuntu0.5 \
-   pkg-config=0.29.1-0ubuntu4 \
-   python3=3.8.2-0ubuntu2 \
-   python3-pytest=4.6.9-1 \
-   tar=1.30+dfsg-7ubuntu0.20.04.4 \
-   tofrodos=1.7.13+ds-4 \
-   unzip=6.0-25ubuntu1.1 \
-   vim=2:8.1.2269-1ubuntu5.31 \
-   wget=1.20.3-1ubuntu2.1 \
-   zlib1g-dev=1:1.2.11.dfsg-2ubuntu1.5
-
+   autoconf=2.71-3 \
+   automake=1:1.16.5-1.3ubuntu1 \
+   build-essential=12.10ubuntu1 \
+   bzip2=1.0.8-5.1build0.1 \
+   cmake=3.28.3-1build7 \
+   curl=8.5.0-2ubuntu10.6 \
+   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 \
+   libgomp1=14.2.0-4ubuntu2~24.04 \
+   libgsl-dev=2.7.1+dfsg-6ubuntu2 \
+   libnss3=2:3.98-1build1 \
+   libpcre2-dev=10.42-4ubuntu2.1 \
+   libxt-dev=1:1.2.1-1.2build1 \
+   pandoc=3.1.3+ds-2 \
+   parallel=20231122+ds-1 \
+   perl=5.38.2-3.2ubuntu0.2 \
+   pkg-config=1.8.1-2build1 \
+   python3=3.12.3-0ubuntu2 \
+   python3-pytest=7.4.4-1 \
+   tar=1.35+dfsg-3build1 \
+   tofrodos=1.7.13+ds-6 \
+   unzip=6.0-28ubuntu4.1 \
+   vim=2:9.1.0016-1ubuntu7.8 \
+   wget=1.21.4-1ubuntu4.1 \
+   zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1
+   
 apt-get clean && rm -rf /var/lib/apt/lists/*
 
 # /usr/bin/python must exist for bgenix, qctool

docker/scripts/install_bcftools.sh

@@ -3,8 +3,8 @@ set -euo pipefail
 
 # deps 
 apt-get update && apt-get install -y --no-install-recommends \
-    libcurl4-gnutls-dev=7.68.0-1ubuntu2.25 \
-    libperl-dev=5.30.0-9ubuntu0.5
+    libcurl4-gnutls-dev=8.5.0-2ubuntu10.6 \
+    libperl-dev=5.38.2-3.2ubuntu0.2
 
 apt-get clean && \
     rm -rf /var/lib/apt/lists/*