Containerize missing tools/update

Fixes #285 Fixes #286
comorment · Dec 31, 2024 · c69f687 · c69f687
1 parent d9da66d
commit c69f687
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Showing 4 changed files with 6 additions and 2 deletions.
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

diff --git a/docker/scripts/R/cran.R b/docker/scripts/R/cran.R
@@ -7,6 +7,7 @@ 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
@@ -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