Containerize tools (#308)

* Containerize tools
Fixes #307

* fix build issues

Author: espenhgn

CHANGELOG.md

@@ -37,6 +37,12 @@ Removed features goes here
 
 Miscellaneous goes here
 
+## [1.11.0] - 2025-09-17
+
+### Added
+
+* added some requested R packages to R container.
+
 ## [1.10.0] - 2025-08-27
 
 ### Updated

docker/scripts/R/bioconductor.R

@@ -24,7 +24,8 @@ packages <- c(
     'limma',
     'org.Hs.eg.db',
     'rtracklayer',
-    'snpStats', 
+    'snpStats',
+    'survcomp',
     'TMixClust',
     'VariantAnnotation')
 

docker/scripts/R/cran.R

@@ -19,6 +19,10 @@ packages <- list(
     'carat',
     'caret',
     'circlize',
+    'coloc',
+    'colocboost',
+    'colocPropTest',
+    'compareC',
     'correlation',
     'corrplot',
     'CPBayes',
@@ -50,6 +54,7 @@ packages <- list(
     'gplots',
     'gtsummary',
     'Haplin',
+    'here',
     'homologene',
     'ieugwasr',
     'imputeMissings',
@@ -74,6 +79,7 @@ packages <- list(
     'PredictABEL',
     'pROC',
     'qqman',
+    'QRISK3',
     'r2redux',
     'reghelper',
     'remotes',

docker/scripts/R/github.R

@@ -26,11 +26,14 @@ packages <- list(
     'MRCIEU/gwasglue' = 'c2d5660eed389e1a9b3e04406b88731d642243f1',
     'noahlorinczcomi/MRBEE' = '6295549a1f5a158c6701eb793646d60c8aef11ca',
     'norment/normentR' = 'dfa1fbae9587db6c3613b0405df4f9cfa98ee0e1',
-    'psychgen/phenotools' = '9eefa4ee0e8ea00bcbdb0e579dcdd7912cfe0597',
+    'psychgen/phenotools' = '62dd11e111d8d952837c9f207557e9b297ba56bc',
     'wouterpeyrot/CCGWAS' = 'ce9764da946189623a0164f156ad119773bc32f5',
     'WSpiller/MVMR' = '65705da9421b6235c7458dba6f01cddfebfe96f5',
     'xiashen/MultiABEL' = '7067fe6753c74f6580029abc82bce914472b4b16',
-    'amorris28/hazrd' = 'f2748a815a094f2e12a5de89c707aa808de5fe25'
+    'amorris28/hazrd' = 'ff9f1690e930792f29e1fd87e25c0dc8632339d5',
+    'cnfoley/hyprcoloc' = '26ea5953a46b3e204dfa8eadd202f746244afa13',
+    'zhenin/HDL/HDL' = '551a8864c5ed3389a6892743ff059357735dc195',
+    'JBPG/Gsens' = '6cac02ba1ccaf38870e2526076f0306c0cf0dc0a'
 )
 
 # install package from GitHub and quit with error if installation fails

docker/scripts/apt_get_essential.sh

@@ -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=2:9.1.0016-1ubuntu7.8 \
+   vim=2:9.1.0016-1ubuntu7.9 \
    wget=1.21.4-1ubuntu4.1 \
    zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1
 

tests/extras/r.R

@@ -12,6 +12,10 @@ libraries_to_check <- c(
     "BiocGenerics",
     "BiocManager",
     "caret",
+    "coloc",
+    "colocboost",
+    "colocPropTest",
+    "compareC",
     "DescTools",
     "devtools",
     "data.table",
@@ -25,6 +29,7 @@ libraries_to_check <- c(
     "ggplot2",
     "gsmr",
     "gtsummary",
+    "here",
     "GWASTools",
     "lightgbm",
     "magrittr",
@@ -33,6 +38,7 @@ libraries_to_check <- c(
     "parameters",
     "PooledCohort",
     "pROC",
+    "QRISK3",
     "qqman",
     "rareGWAMA",
     "reghelper",
@@ -91,13 +97,15 @@ libraries_to_check <- c(
     "glmnet",
     "gplots",
     "gridExtra",
+    "Gsens",
     "gwasglue",
     "gwasglue2",
     "gwasurvivr",
     "gwasvcf",
     "haven",
     "Haplin",
     "hazrd",
+    "HDL",
     "homologene",
     "hyprcoloc",
     "ieugwasr",
@@ -149,6 +157,7 @@ libraries_to_check <- c(
     "splines2",
     "stats",
     "stats4",
+    "survcomp",
     "survival",
     "survminer",
     "tidyverse",

version/version.py

@@ -1,5 +1,5 @@
 _MAJOR = "1"
-_MINOR = "10"
+_MINOR = "11"
 # On main and in a nightly release the patch should be one ahead of the last
 # released build.
 _PATCH = "0"