diff --git a/CHANGELOG.md b/CHANGELOG.md index 2b41f967..ce1dcf1e 100644 --- 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 index 8bf4b243..cce54a48 100644 --- 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 index 3271e014..670092cd 100644 --- 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 index 49da63a0..315e2354 100644 --- 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