Containerize missing tools/update (#289)

* Containerize missing tools/update Fixes #285 Fixes #286 * bump ubuntu package versions * bioconductor date * bumps * change date 09.04 for posit packs * date * test * ask=False
comorment · Dec 31, 2024 · 89ffdf4 · 89ffdf4
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,6 +21,7 @@ If MD5 sum is not listed for a certain release then it means that the container
 
 ### Added
 
+* Add R packages AER, MendelianRandomization, gwasurvivr
 * Add R packages lightgbm, EFAtools, RiskScorescvd, glmnet, survival, caret, PooledCohort, genio, HyPrColoc
 * Add Python3 packages miniwdl, miniwdl-slurm, dxpy
 * Add unit test runs as part of the GitHub Actions workflow for building Docker containers

diff --git a/docker/dockerfiles/r/Dockerfile b/docker/dockerfiles/r/Dockerfile
@@ -1,5 +1,5 @@
 # R container
-FROM rocker/verse:4.4.1
+FROM ghcr.io/rocker-org/verse:4.4.1
 # based on Ubuntu 22.04.5 LTS (jammy)
 
 ENV TZ=Europe
@@ -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/2024-09-01', dependencies=c('Depends', 'Imports', 'LinkingTo'))"
+RUN R -e "install.packages('devtools', repos='https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-04', dependencies=c('Depends', 'Imports', 'LinkingTo'))"
 COPY /scripts/R/cran.R .
 RUN Rscript cran.R
 

diff --git a/docker/scripts/R/bioconductor.R b/docker/scripts/R/bioconductor.R
@@ -2,13 +2,13 @@
 dependencies <- c('Depends', 'Imports', 'LinkingTo')
 upgrade <- 'default'
 
-url = "https://packagemanager.posit.co/bioconductor/__linux__/jammy/2024-09-02"
+url = "https://packagemanager.posit.co/bioconductor/__linux__/jammy/2024-09-04"
 # Configure BioCManager to use Posit Package Manager:
-options(BioC_mirror = "https://packagemanager.posit.co/bioconductor/2024-09-02")
-options(BIOCONDUCTOR_CONFIG_FILE = "https://packagemanager.posit.co/bioconductor/2024-09-02/config.yaml")
+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")
 
 # Configure a CRAN snapshot compatible with Bioconductor 3.19:
-options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-01"))
+options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-04"))
 
 # Bioconductor packages
 packages <- c(
@@ -29,6 +29,8 @@ packages <- c(
 
 # install package from Bioconductor and quit with error if installation fails
 library(devtools)
+BiocManager::install(version='3.19', ask=FALSE)
+
 for (package in packages) {
     tryCatch(
     {

diff --git a/docker/scripts/R/cran.R b/docker/scripts/R/cran.R
@@ -1,12 +1,13 @@
 require(devtools)
-url <- "https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-01"
+url <- "https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-04"
 dependencies <- c('Depends', 'Imports', 'LinkingTo')
 upgrade <- 'default'
 
 options(repos = c(CRAN = url))
 
 # CRAN packages w. version
 packages <- list(
+    'AER',
     'argparser',
     'arsenal',
     'bigreadr',
@@ -54,6 +55,7 @@ packages <- list(
     'lmerTest',
     'magrittr',
     'MatrixEQTL',
+    'MendelianRandomization',
     'mgcv',  # has gamm function
     'miniCRAN',
     'moments',

diff --git a/docker/scripts/R/github.R b/docker/scripts/R/github.R
@@ -1,4 +1,4 @@
-url <- "https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-01"
+url <- "https://packagemanager.posit.co/cran/__linux__/jammy/2024-09-04"
 dependencies <- c('Depends', 'Imports', 'LinkingTo')
 upgrade <- 'default'
 auth_token <- Sys.getenv("github_pat")
@@ -28,7 +28,8 @@ packages <- list(
     'psychgen/phenotools' = '9eefa4ee0e8ea00bcbdb0e579dcdd7912cfe0597',
     'wouterpeyrot/CCGWAS' = 'ce9764da946189623a0164f156ad119773bc32f5',
     'WSpiller/MVMR' = '65705da9421b6235c7458dba6f01cddfebfe96f5',
-    'xiashen/MultiABEL' = '7067fe6753c74f6580029abc82bce914472b4b16'
+    'xiashen/MultiABEL' = '7067fe6753c74f6580029abc82bce914472b4b16',
+    'suchestoncampbelllab/gwasurvivr' = 'adad8509ad5f1f3033548bcb4d00f6f9c60778fa'
 )
 
 # install package from GitHub and quit with error if installation fails

diff --git a/docker/scripts/apt_get_essential.sh b/docker/scripts/apt_get_essential.sh
@@ -12,14 +12,14 @@ apt-get update && apt-get install -y --no-install-recommends \
    build-essential=12.8ubuntu1 \
    bzip2=1.0.8-2 \
    cmake=3.16.3-1ubuntu1.20.04.1 \
-   curl=7.68.0-1ubuntu2.24 \
+   curl=7.68.0-1ubuntu2.25 \
    dos2unix=7.4.0-2 \
    gdb=9.1-0ubuntu1 \
    gfortran=4:9.3.0-1ubuntu2 \
    git=1:2.25.1-1ubuntu3.13 \
    less=551-1ubuntu0.3 \
    libatlas-base-dev=3.10.3-8ubuntu7 \
-   libcurl4-openssl-dev=7.68.0-1ubuntu2.24 \
+   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 \
@@ -35,7 +35,7 @@ apt-get update && apt-get install -y --no-install-recommends \
    tar=1.30+dfsg-7ubuntu0.20.04.4 \
    tofrodos=1.7.13+ds-4 \
    unzip=6.0-25ubuntu1.1 \
-   vim=2:8.1.2269-1ubuntu5.25 \
+   vim=2:8.1.2269-1ubuntu5.29 \
    wget=1.20.3-1ubuntu2.1 \
    zlib1g-dev=1:1.2.11.dfsg-2ubuntu1.5
 

diff --git a/docker/scripts/install_bcftools.sh b/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=7.68.0-1ubuntu2.24 \
+    libcurl4-gnutls-dev=7.68.0-1ubuntu2.25 \
     libperl-dev=5.30.0-9ubuntu0.5
 
 apt-get clean && \

diff --git a/docker/scripts/install_minimac4.sh b/docker/scripts/install_minimac4.sh
@@ -4,7 +4,7 @@ set -euo pipefail
 # install some deps for installing cget
 apt-get update && \
     apt-get install --no-install-recommends \
-    python3-pip=20.0.2-5ubuntu1.10 \
+    python3-pip=20.0.2-5ubuntu1.11 \
     python3-click=7.0-3 \
     python3-six=1.14.0-2 \
     -y && \

diff --git a/tests/extras/r.R b/tests/extras/r.R
@@ -5,6 +5,7 @@ library(testthat)
 
 # List of libraries to check
 libraries_to_check <- c(
+    "AER",
     "argparser", 
     "bigreadr", 
     "bigsnpr",
@@ -90,6 +91,7 @@ libraries_to_check <- c(
     "gridExtra",
     "gwasglue",
     "gwasglue2",
+    "gwasurvivr",
     "gwasvcf",
     "haven",
     "Haplin",
@@ -105,6 +107,7 @@ libraries_to_check <- c(
     "lubridate",
     "MASS",
     "MatrixEQTL",
+    "MendelianRandomization",
     "mgcv",
     "miniCRAN",
     "MRBEE",