From 03fccf724c17e8c58acd3566ccd7dc725b6d85ee Mon Sep 17 00:00:00 2001 From: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Mon, 8 Jun 2026 09:57:55 +0200 Subject: [PATCH 1/7] Update/add software Fixes #323 --- CHANGELOG.md | 7 + docker/dockerfiles/python3/Dockerfile | 6 +- docker/dockerfiles/r/Dockerfile | 2 +- docker/scripts/R/cran.R | 247 +++++++++++++------------- docker/scripts/R/github.R | 6 +- docker/scripts/apt_get_essential.sh | 6 +- tests/extras/r.R | 170 +++++++++--------- tests/test_python3.py | 3 + version/version.py | 2 +- 9 files changed, 240 insertions(+), 209 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 368af11a..d6a396d1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -37,6 +37,13 @@ Removed features goes here Miscellaneous goes here +## 1.16.0 - 2026-06-08 + +### Added + +* Added R packages: mirt, PerformanceAnalytics, tidymodels, splitstackshape, fastDummies, pbapply, kernlab, PheWAS +* Added Python packages pymoo, paretoset, pyhazrd + ## 1.15.0 - 2026-02-23 ### Added diff --git a/docker/dockerfiles/python3/Dockerfile b/docker/dockerfiles/python3/Dockerfile index 97061ec1..1f8052bc 100644 --- a/docker/dockerfiles/python3/Dockerfile +++ b/docker/dockerfiles/python3/Dockerfile @@ -59,6 +59,7 @@ RUN mamba install python=3.12.12 \ psycopg2=2.9.11 \ pyarrow=22.0.0 \ pydot=4.0.1 \ + pymoo=0.6.1.5 \ pymysql=1.1.2 \ pyqt=5.15.11 \ pyreadr=0.5.4 \ @@ -98,13 +99,16 @@ RUN pip install --no-cache-dir --no-deps \ hdf5storage==0.2.2 \ LDpred==1.0.11 \ Pgenlib==0.93.0 \ + paretoset==1.2.5 \ plinkio==0.9.8 \ plinkliftover==0.5.2 \ poetry==2.2.1 \ pooch==1.8.2 \ pycap==2.7.0 \ pyliftover==0.4.1 \ - pysnptools==0.5.14 && \ + pysnptools==0.5.14 \ + git+https://github.com/espenhgn/hazrd/tree/copilot/convert-hazrd-to-pyhazrd \ + && \ pip cache purge # Plink (as python_convert depends on plink) diff --git a/docker/dockerfiles/r/Dockerfile b/docker/dockerfiles/r/Dockerfile index 28ac1279..b3d4e7f4 100644 --- a/docker/dockerfiles/r/Dockerfile +++ b/docker/dockerfiles/r/Dockerfile @@ -17,7 +17,7 @@ RUN apt-get update -y && apt-get install -y --no-install-recommends \ rm -rf /var/lib/apt/lists/* RUN apt-get update -y && apt-get install -y --no-install-recommends \ - curl=8.5.0-2ubuntu10.6 \ + curl=8.5.0-2ubuntu10.9 \ libperl-dev=5.38.2-3.2ubuntu0.2 \ libgslcblas0=2.7.1+dfsg-6ubuntu2 \ lmodern=2.005-1 \ diff --git a/docker/scripts/R/cran.R b/docker/scripts/R/cran.R index ca732476..29ac9e43 100644 --- a/docker/scripts/R/cran.R +++ b/docker/scripts/R/cran.R @@ -1,129 +1,136 @@ require(devtools) url <- "https://packagemanager.posit.co/cran/__linux__/noble/2025-08-01" -dependencies <- c('Depends', 'Imports', 'LinkingTo') -upgrade <- 'default' +dependencies <- c("Depends", "Imports", "LinkingTo") +upgrade <- "default" options(repos = c(CRAN = url)) # CRAN packages w. version packages <- list( - 'AER', - 'argparser', - 'arsenal', - 'arrow', - 'bdsmatrix', - 'bigreadr', - 'bigsnpr', - 'BiocManager', - 'bit', - 'bit64', - 'brant', - 'brms', - 'carat', - 'caret', - 'circlize', - 'coloc', - 'colocboost', - 'colocPropTest', - 'compareC', - 'correlation', - 'corrplot', - 'coxme', - 'CPBayes', - 'DescTools', - 'data.table', - 'dendextend', - 'dplyr', - 'EFAtools', - 'egg', - 'fastICA', - 'fcfdr', - 'feather', - 'flextable', - 'fmsb', - 'foreign', - 'GCPBayes', - 'geepack', - 'genio', - 'ggalluvial', - 'ggcorrplot', - 'ggplot2', - 'ggpubr', - 'ggrepel', - 'ggseg', - 'ggseg3d', - 'ggstar', - 'ggthemes', - 'ggpubr', - 'gitcreds', - 'glmmTMB', - 'glmnet', - 'glue', - 'gplots', - 'gtsummary', - 'Haplin', - 'here', - 'homologene', - 'ieugwasr', - 'imputeMissings', - 'jtools', - 'kinship2', - 'lavaan', - 'lightgbm', - 'lmerTest', - 'magrittr', - 'matlab', - 'matlab2r', - 'MatrixEQTL', - 'matrixStats', - 'MendelianRandomization', - 'mgcv', # has gamm function - 'miniCRAN', - 'moments', - 'MplusAutomation', - 'MVN', - 'mvtnorm', - 'optparse', - 'parameters', - 'patchwork', - 'pgenlibr', - 'PooledCohort', - 'pracma', - 'PredictABEL', - 'pROC', - 'psych', - 'qqman', - 'QRISK3', - 'r2redux', - 'reghelper', - 'remotes', - 'RiskScorescvd', - 'rjags', - 'rmatio', - 'R.matlab', - 'ROCR', - 'rmarkdown', - 'rstan', - 'runonce', - 'scales', - 'semptools', - 'seqminer', - 'semTools', - 'simplecolors', - 'simsalapar', - 'sp', - 'splines2', - 'stringr', - 'susieR', - 'survey', - 'survival', - 'survminer', - 'tibble', - 'tidyr', - 'tree', - 'vctrs', - 'xgboost', - 'zlib') + "AER", + "BiocManager", + "CPBayes", + "DescTools", + "EFAtools", + "GCPBayes", + "Haplin", + "MVN", + "MatrixEQTL", + "MendelianRandomization", + "MplusAutomation", + "PerformanceAnalytics", + "PooledCohort", + "PredictABEL", + "QRISK3", + "R.matlab", + "ROCR", + "RiskScorescvd", + "argparser", + "arrow", + "arsenal", + "bdsmatrix", + "bigreadr", + "bigsnpr", + "bit", + "bit64", + "brant", + "brms", + "carat", + "caret", + "circlize", + "coloc", + "colocPropTest", + "colocboost", + "compareC", + "correlation", + "corrplot", + "coxme", + "data.table", + "dendextend", + "dplyr", + "egg", + "fastDummies", + "fastICA", + "fcfdr", + "feather", + "flextable", + "fmsb", + "foreign", + "geepack", + "genio", + "ggalluvial", + "ggcorrplot", + "ggplot2", + "ggpubr", + "ggpubr", + "ggrepel", + "ggseg", + "ggseg3d", + "ggstar", + "ggthemes", + "gitcreds", + "glmmTMB", + "glmnet", + "glue", + "gplots", + "gtsummary", + "here", + "homologene", + "ieugwasr", + "imputeMissings", + "jtools", + "kernlab", + "kinship2", + "lavaan", + "lightgbm", + "lmerTest", + "magrittr", + "matlab", + "matlab2r", + "matrixStats", + "mgcv", + "miniCRAN", + "mirt", + "moments", + "mvtnorm", + "optparse", + "pbapply", + "pROC", + "parameters", + "patchwork", + "pgenlibr", + "pracma", + "psych", + "qqman", + "r2redux", + "reghelper", + "remotes", + "rjags", + "rmarkdown", + "rmatio", + "rstan", + "runonce", + "scales", + "semTools", + "semptools", + "seqminer", + "simplecolors", + "simsalapar", + "sp", + "splines2", + "splitstackshape", + "stringr", + "survey", + "survival", + "survminer", + "susieR", + "tibble", + "tidymodels", + "tidyr", + "tree", + "vctrs", + "xgboost", + "zlib") # install package from CRAN and quit with error if installation fails @@ -138,7 +145,7 @@ for (package in packages) { error = function(e) { cat("Error occurred during package installation:\n") print(e) - quit(status=1, save='no') + quit(status=1, save="no") }, finally = { } diff --git a/docker/scripts/R/github.R b/docker/scripts/R/github.R index e5f69a58..2ee883e9 100644 --- a/docker/scripts/R/github.R +++ b/docker/scripts/R/github.R @@ -33,7 +33,7 @@ packages <- list( "wouterpeyrot/CCGWAS" = "ce9764da946189623a0164f156ad119773bc32f5", "WSpiller/MVMR" = "65705da9421b6235c7458dba6f01cddfebfe96f5", "xiashen/MultiABEL" = "7067fe6753c74f6580029abc82bce914472b4b16", - "amorris28/hazrd" = "ff9f1690e930792f29e1fd87e25c0dc8632339d5", + "amorris28/hazrd" = "c75b2f12361d98f4c50841ec67190e9e7b14c322", "cnfoley/hyprcoloc" = "26ea5953a46b3e204dfa8eadd202f746244afa13", "zhenin/HDL/HDL" = "551a8864c5ed3389a6892743ff059357735dc195", "JBPG/Gsens" = "6cac02ba1ccaf38870e2526076f0306c0cf0dc0a", @@ -41,7 +41,9 @@ packages <- list( "mrcieu/gwasglue2" = "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa", "gqi/MRMix" = "56afdb2bc96760842405396f5d3f02e60e305039", "JianYang-Lab/gsmr2" = "e7953cc136ad1cfae14674facde21e90caddea5f", - "n-mounier/MRlap" = "660f026864f8bfbbad5a8206bdff7d58f5d5d05b") + "n-mounier/MRlap" = "660f026864f8bfbbad5a8206bdff7d58f5d5d05b", + "PheWAS/PheWAS" = "55dd1c24e228851922400cfba8d7db474565ccc7") + # install package from GitHub and quit with error if installation fails for (package in names(packages)) { diff --git a/docker/scripts/apt_get_essential.sh b/docker/scripts/apt_get_essential.sh index a5594476..ff3da242 100644 --- 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=12.10ubuntu1 \ bzip2=1.0.8-5.1build0.1 \ cmake=3.28.3-1build7 \ - curl=8.5.0-2ubuntu10.6 \ + curl=8.5.0-2ubuntu10.9 \ 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 \ + libcurl4-openssl-dev=8.5.0-2ubuntu10.9 \ libgomp1=14.2.0-4ubuntu2~24.04.1 \ libgsl-dev=2.7.1+dfsg-6ubuntu2 \ libnss3=2:3.98-1build1 \ @@ -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=2:9.1.0016-1ubuntu7.9 \ + vim=2:9.1.0016-1ubuntu7.14 \ wget=1.21.4-1ubuntu4.1 \ zlib1g-dev=1:1.3.dfsg-3.1ubuntu2.1 diff --git a/tests/extras/r.R b/tests/extras/r.R index 91887a94..bb1bed54 100644 --- a/tests/extras/r.R +++ b/tests/extras/r.R @@ -6,93 +6,89 @@ library(testthat) # List of libraries to check libraries_to_check <- c( "AER", - "argparser", - "bdsmatrix", - "bigreadr", - "bigsnpr", + "ASSET", + "AnnotationDbi", "BiocGenerics", "BiocManager", - "bit", - "bit64", - "caret", - "coloc", - "colocboost", - "colocPropTest", - "compareC", + "CCGWAS", + "CPBayes", + "DBI", "DescTools", - "devtools", - "data.table", - "dplyr", "EFAtools", - "egg", - "feather", - "flextable", - "fmsb", - "foreign", - "genio", - "GenomicSEM", - "ggplot2", - "gsmr", - "gtsummary", - "here", + "GCPBayes", "GWASTools", - "lightgbm", - "magrittr", - "mvtnorm", - "optparse", - "parameters", + "GenomicSEM", + "Gsens", + "HDL", + "Haplin", + "MASS", + "MRBEE", + "MRlap", + "MVMR", + "MVN", + "MatrixEQTL", + "MendelianRandomization", + "MplusAutomation", + "MultiABEL", + "PerformanceAnalytics", + "PheWAS", "PooledCohort", - "pROC", + "PredictABEL", "QRISK3", - "qqman", - "rareGWAMA", - "reghelper", - "regtools", - "remotes", + "R.matlab", + "RColorBrewer", + "ROCR", + "RSQLite", + "Rcpp", "RiskScorescvd", - "rmarkdown", - "runonce", - "snpStats", - "survey", - "seqminer", - "stringr", - "tibble", - "tidyr", - "tidyverse", - "tools", + "TMixClust", "TwoSampleMR", - "xgboost", - "zlib", - "AnnotationDbi", + "argparser", "arsenal", - "ASSET", + "bdsmatrix", + "bigreadr", + "bigsnpr", "biomaRt", "biomartr", + "bit", + "bit64", "brant", "brms", "broom", - "carat", "car", - "CCGWAS", + "carat", + "caret", "cfdr", - "cfdrCommonControls", "cfdr.pleio", + "cfdrCommonControls", "circlize", "clusterProfiler", + "coloc", + "colocPropTest", + "colocboost", + "compareC", "correlation", "corrplot", "coxme", - "CPBayes", - "DBI", + "data.table", "dendextend", + "devtools", + "dplyr", "e1071", + "egg", + "fastDummies", "fastICA", "fcfdr", + "feather", + "flextable", + "fmsb", + "foreign", "foreign", - "GCPBayes", "geepack", + "genio", "ggalluvial", "ggcorrplot", + "ggplot2", "ggpubr", "ggrepel", "ggseg", @@ -105,84 +101,96 @@ libraries_to_check <- c( "glmnet", "gplots", "gridExtra", - "Gsens", + "gsmr", "gsmr2", + "gtsummary", "gwasglue", "gwasglue2", "gwasurvivr", "gwasvcf", "haven", - "Haplin", "hazrd", - "HDL", + "here", "homologene", "hyprcoloc", "ieugwasr", "imputeMissings", "jtools", + "kernlab", + "kinship2", "lavaan", + "lightgbm", "limma", "lme4", "lmerTest", "lubridate", - "kinship2", - "MASS", + "magrittr", "matlab", "matlab2r", - "MatrixEQTL", "matrixStats", - "MendelianRandomization", "mgcv", "miniCRAN", - "MRBEE", - "MRlap", - "MVMR", + "mirt", "modelr", "moments", - "MplusAutomation", "mr.raps", - "MultiABEL", - "MVN", + "mvtnorm", "nlme", "normentR", "officer", + "optparse", "org.Hs.eg.db", + "pROC", "parallel", + "parameters", "patchwork", + "pbapply", "pgenlibr", "phenotools", "pracma", - "PredictABEL", "psych", - "rhdf5", - "R.matlab", - "rmatio", - "RColorBrewer", - "Rcpp", - "readxl", + "qqman", + "rareGWAMA", "readr", + "readxl", + "reghelper", + "regtools", + "remotes", + "rhdf5", "rjags", - "ROCR", - "RSQLite", + "rmarkdown", + "rmatio", "rstan", "rtracklayer", + "runonce", "scales", - "semptools", "semTools", + "semptools", + "seqminer", "simplecolors", "simsalapar", + "snpStats", "sp", "splines", "splines2", + "splitstackshape", "stats", "stats4", + "stringr", "survcomp", + "survey", "survival", "survminer", + "tibble", + "tidymodels", + "tidyr", "tidyverse", - "TMixClust", + "tidyverse", + "tools", "tree", - "viridis") + "viridis", + "xgboost", + "zlib") # Define a test diff --git a/tests/test_python3.py b/tests/test_python3.py index 3f456348..2cbce538 100644 --- a/tests/test_python3.py +++ b/tests/test_python3.py @@ -137,11 +137,14 @@ def test_python3_packages(): 'pandas_gbq', 'pandas_plink', 'paramiko', + 'paretoset', 'plinkio', 'psycopg2', 'pyarrow', 'pydot', + 'pyhazrd', 'pyliftover', + 'pymoo', 'pymysql', 'PyQt5', 'pyreadr', diff --git a/version/version.py b/version/version.py index 3db9b64c..be7a3b61 100644 --- a/version/version.py +++ b/version/version.py @@ -1,5 +1,5 @@ _MAJOR = "1" -_MINOR = "15" +_MINOR = "16" # On main and in a nightly release the patch should be one ahead of the last # released build. _PATCH = "0" From f340a2fdfebbe64893d5d86799326969161c9bf2 Mon Sep 17 00:00:00 2001 From: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Mon, 8 Jun 2026 10:11:59 +0200 Subject: [PATCH 2/7] fix build Fixes #323 --- .github/workflows/docker.yml | 2 +- docker/dockerfiles/python3/Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index 8afe18d0..f2775280 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -10,7 +10,7 @@ jobs: - name: Check out code uses: actions/checkout@v3 - name: hadolint - uses: reviewdog/action-hadolint@v1 + uses: reviewdog/action-hadolint@v3.1.0 with: reporter: github-pr-review # Default is github-pr-check fail_on_error: true diff --git a/docker/dockerfiles/python3/Dockerfile b/docker/dockerfiles/python3/Dockerfile index 1f8052bc..86d8ba0a 100644 --- a/docker/dockerfiles/python3/Dockerfile +++ b/docker/dockerfiles/python3/Dockerfile @@ -107,7 +107,7 @@ RUN pip install --no-cache-dir --no-deps \ pycap==2.7.0 \ pyliftover==0.4.1 \ pysnptools==0.5.14 \ - git+https://github.com/espenhgn/hazrd/tree/copilot/convert-hazrd-to-pyhazrd \ + git+https://github.com/espenhgn/hazrd.git@copilot/convert-hazrd-to-pyhazrd \ && \ pip cache purge From b904fad17c3143b9f78f6c53941013ba612104a1 Mon Sep 17 00:00:00 2001 From: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Mon, 8 Jun 2026 10:22:12 +0200 Subject: [PATCH 3/7] reviewdog/hadolint version --- .github/workflows/docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index f2775280..4511e515 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -10,7 +10,7 @@ jobs: - name: Check out code uses: actions/checkout@v3 - name: hadolint - uses: reviewdog/action-hadolint@v3.1.0 + uses: reviewdog/action-hadolint@v1.50.5 with: reporter: github-pr-review # Default is github-pr-check fail_on_error: true From f7e067f5102b7992b751c0f7e79eb716199000ae Mon Sep 17 00:00:00 2001 From: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Mon, 8 Jun 2026 11:54:20 +0200 Subject: [PATCH 4/7] test --- docker/scripts/install_king.sh | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/docker/scripts/install_king.sh b/docker/scripts/install_king.sh index 9e39522f..dd8a407a 100644 --- a/docker/scripts/install_king.sh +++ b/docker/scripts/install_king.sh @@ -3,10 +3,13 @@ set -euo pipefail # king VERSION="232" -wget --debug --no-check-certificate --user-agent="Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/83.0.4103.61 Chrome/83.0.4103.61 Safari/537.36" https://www.kingrelatedness.com/executables/Linux-king$VERSION.tar.gz && \ +wget --debug --no-check-certificate \ + -nv --https-only --retry-connrefused --waitretry=2 --tries=5 --timeout=30 \ + --user-agent="Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/83.0.4103.61 Chrome/83.0.4103.61 Safari/537.36" \ + https://www.kingrelatedness.com/executables/Linux-king$VERSION.tar.gz && \ tar -xvzf Linux-king$VERSION.tar.gz && \ rm -rf Linux-king$VERSION.tar.gz -cp king /bin +cp king /bin rm -rf * \ No newline at end of file From 54d70e8cccac5615f9192ed81a643f5d390f3c4d Mon Sep 17 00:00:00 2001 From: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Mon, 8 Jun 2026 12:02:52 +0200 Subject: [PATCH 5/7] drop KING relatedness software --- CHANGELOG.md | 4 ++++ docker/dockerfiles/gwas/Dockerfile | 8 ++++---- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d6a396d1..b65511d0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -43,6 +43,10 @@ Miscellaneous goes here * Added R packages: mirt, PerformanceAnalytics, tidymodels, splitstackshape, fastDummies, pbapply, kernlab, PheWAS * Added Python packages pymoo, paretoset, pyhazrd + +### Removed + +* drop KING relatedness software from gwas build, due to issues with downloading the binary and lack of updates from the developer ## 1.15.0 - 2026-02-23 diff --git a/docker/dockerfiles/gwas/Dockerfile b/docker/dockerfiles/gwas/Dockerfile index 69afd7cb..07c22fd3 100644 --- a/docker/dockerfiles/gwas/Dockerfile +++ b/docker/dockerfiles/gwas/Dockerfile @@ -72,10 +72,10 @@ RUN bash /tmp/snptest/install_snptest.sh && \ rm -rf /tmp/snptest # king -WORKDIR /tmp/king -COPY /scripts/install_king.sh /tmp/king/ -RUN bash /tmp/king/install_king.sh && \ - rm -rf /tmp/king +# WORKDIR /tmp/king +# COPY /scripts/install_king.sh /tmp/king/ +# RUN bash /tmp/king/install_king.sh && \ +# rm -rf /tmp/king # ldak WORKDIR /tmp/ldak From 9f495e0df2cd7d9e374e98b5088964dfae05c753 Mon Sep 17 00:00:00 2001 From: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Mon, 8 Jun 2026 13:28:58 +0200 Subject: [PATCH 6/7] version pins --- docker/scripts/install_htslib.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker/scripts/install_htslib.sh b/docker/scripts/install_htslib.sh index f6d4a830..9a3cc5f8 100644 --- a/docker/scripts/install_htslib.sh +++ b/docker/scripts/install_htslib.sh @@ -4,8 +4,8 @@ set -euo pipefail # additional deps apt-get update && apt-get install --no-install-recommends \ libbz2-dev=1.0.8-5.1build0.1 \ - liblzma-dev=5.6.1+really5.4.5-1ubuntu0.2 \ - libssl-dev=3.0.13-0ubuntu3.7 \ + liblzma-dev=5.6.1+really5.4.5-1ubuntu0.3 \ + libssl-dev=3.0.13-0ubuntu3.9 \ -y apt-get clean && \ From cc087680481d84bdf3317e660f2f155621dcc258 Mon Sep 17 00:00:00 2001 From: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Mon, 8 Jun 2026 13:37:54 +0200 Subject: [PATCH 7/7] version pin bump --- docker/scripts/install_bcftools.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/scripts/install_bcftools.sh b/docker/scripts/install_bcftools.sh index fbf9573a..fcc2ce8f 100644 --- 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=8.5.0-2ubuntu10.6 \ + libcurl4-gnutls-dev=8.5.0-2ubuntu10.9 \ libperl-dev=5.38.2-3.2ubuntu0.2 apt-get clean && \