Add/update software

Fixes #315

Author: espenhgn

CHANGELOG.md

@@ -37,6 +37,13 @@ Removed features goes here
 
 Miscellaneous goes here
 
+## 1.15.0 - 2026-02-23
+
+### Added
+
+* Added `OPERA` tool to `gwas.sif` container, with corresponding test.
+* Added Python and R packages to `python3.sif` and `r.sif` containers, with corresponding test.
+
 ## 1.14.0 - 2025-12-05
 
 ### Updated

docker/dockerfiles/gwas/Dockerfile

@@ -202,4 +202,12 @@ COPY /scripts/install_liftover.sh /tmp/liftover/
 RUN bash /tmp/liftover/install_liftover.sh && \
     rm -rf /tmp/liftover
 
+
+# OPERA
+WORKDIR /tmp/opera
+RUN wget https://github.com/wuyangf7/OPERA/blob/main/opera_Linux.zip?raw=true -O opera_Linux.zip && \
+    unzip opera_Linux.zip && \
+    rm opera_Linux.zip && \
+    mv opera_Linux/opera_Linux /usr/bin/opera
+
 WORKDIR /tools

docker/dockerfiles/python3/Dockerfile

@@ -22,14 +22,21 @@ RUN conda install mamba -n base -c conda-forge && \
 # keep the list of packages sorted alphabetically
 # https://www.online-utility.org/text/sort.jsp
 RUN mamba install python=3.12.12 \
+    BeautifulSoup4=4.14.3 \
+    bottleneck=1.6.0 \
     configparser=7.2.0 \
     dask=2025.11.0 \
     fastparquet=2024.11.0 \
+    fsspec=2026.2.0 \
+    gcsfs=2026.2.0 \
     graphviz=14.0.5 \
     "h5py=3.15.1=nompi*" \
+    html5lib=1.1 \
+    Jinja2=3.1.6 \
     jupyterlab=4.5.0 \
     lightgbm=4.6.0 \
     lifelines=0.30.0 \
+    lxml=6.0.2 \
     imbalanced-learn=0.14.0 \
     intervaltree=3.1.0 \
     matplotlib-venn=1.1.2 \
@@ -40,27 +47,42 @@ RUN mamba install python=3.12.12 \
     networkx=3.6 \
     numdifftools=0.9.41 \
     numba=0.62.1 \
+    numexpr=2.14.1 \
     numpy=2.3.5 \
+    odfpy=1.4.1 \
     openpyxl=3.1.5 \
     pandas=2.3.3 \
+    pandas-gbq=0.28.0 \
     pandas-plink=2.3.2 \
     paramiko=4.0.0 \
     psutil=7.1.3 \
+    psycopg2=2.9.11 \
     pyarrow=22.0.0 \
     pydot=4.0.1 \
+    pymysql=1.1.2 \
+    pyqt=5.15.11 \
+    pyreadr=0.5.4 \
     pyreadstat=1.3.2 \
     pytables=3.10.2 \
     python-graphviz=0.21 \
+    python-blosc2=4.0.0 \
+    pyxlsb=1.0.10 \
     pyyaml=6.0.3 \
+    qtpy=2.4.3 \
+    s3fs=2026.2.0 \
     scikit-learn=1.7.2 \
     scikit-survival=0.25.0 \
     scipy=1.16.3 \
     seaborn=0.13.2 \
     semantic_version=2.10.0 \
     shap=0.48.0 \
     statsmodels=0.14.5 \
+    SQLAlchemy=2.0.46 \
+    tabulate=0.9.0 \
+    xarray=2026.2.0 \
     xgboost=3.1.2 \
     xlrd=2.0.2 \
+    xlsxwriter=3.2.9 \
     xmltodict=1.0.2 \
     --yes && \
     mamba clean -a -y

docker/scripts/R/cran.R

@@ -72,6 +72,8 @@ packages <- list(
     'lightgbm',
     'lmerTest',
     'magrittr',
+    'matlab',
+    'matlab2r',
     'MatrixEQTL',
     'matrixStats',
     'MendelianRandomization',
@@ -93,10 +95,14 @@ packages <- list(
     'qqman',
     'QRISK3',
     'r2redux',
+    'raveio',
     'reghelper',
     'remotes',
+    'rhdf5',
     'RiskScorescvd',
     'rjags',
+    'rmatio',
+    'R.matlab',
     'ROCR',
     'rmarkdown',
     'rstan',
@@ -120,6 +126,7 @@ packages <- list(
     'vctrs',
     'xgboost',
     'zlib')
+
 
 # install package from CRAN and quit with error if installation fails
 # for (package in names(packages)) {

docker/scripts/R/github.R

@@ -26,6 +26,7 @@ packages <- list(
     "qingyuanzhao/mr.raps" = "27b96f31e26ae97a395422bd757f514a7f96cc85",
     "MRCIEU/TwoSampleMR" = "578c68fa754c57d764553812bf85d69ecf43b011",
     "MRCIEU/gwasglue" = "c2d5660eed389e1a9b3e04406b88731d642243f1",
+    # misc
     "noahlorinczcomi/MRBEE" = "6295549a1f5a158c6701eb793646d60c8aef11ca",
     "norment/normentR" = "dfa1fbae9587db6c3613b0405df4f9cfa98ee0e1",
     "psychgen/phenotools" = "62dd11e111d8d952837c9f207557e9b297ba56bc",
@@ -38,8 +39,11 @@ packages <- list(
     "JBPG/Gsens" = "6cac02ba1ccaf38870e2526076f0306c0cf0dc0a",
     "MRCIEU/genetics.binaRies" = "2fcd3ee3088b729c7eb34cf2aac9dc2e04fe4412",
     "mrcieu/gwasglue2" = "c93b3a1fca7d2eae5d40bd62117091b1ad57f0fa",
-    "gqi/MRMix" = "56afdb2bc96760842405396f5d3f02e60e305039")
-
+    "gqi/MRMix" = "56afdb2bc96760842405396f5d3f02e60e305039",
+    "JianYang-Lab/gsmr2" = "e7953cc136ad1cfae14674facde21e90caddea5f",
+    "n-mounier/MRlap" = "660f026864f8bfbbad5a8206bdff7d58f5d5d05b")
+    
+    
 # install package from GitHub and quit with error if installation fails
 for (package in names(packages)) {
     ref <- packages[[package]]

docker/scripts/apt_get_essential.sh

@@ -20,7 +20,7 @@ apt-get update && apt-get install -y --no-install-recommends \
    less=590-2ubuntu2.1 \
    libatlas-base-dev=3.10.3-13ubuntu1 \
    libcurl4-openssl-dev=8.5.0-2ubuntu10.6 \
-   libgomp1=14.2.0-4ubuntu2~24.04 \
+   libgomp1=14.2.0-4ubuntu2~24.04.1 \
    libgsl-dev=2.7.1+dfsg-6ubuntu2 \
    libnss3=2:3.98-1build1 \
    libpcre2-dev=10.42-4ubuntu2.1 \

docker/scripts/install_eagle.sh

@@ -2,7 +2,7 @@
 set -euo pipefail
 
 apt-get update && apt-get install --no-install-recommends \
-    libopenblas-dev=0.3.26+ds-1 \
+    libopenblas-dev=0.3.26+ds-1ubuntu0.1 \
     -y && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*

docker/scripts/install_htslib.sh

@@ -5,7 +5,7 @@ set -euo pipefail
 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=3.0.13-0ubuntu3.6 \
+    libssl-dev=3.0.13-0ubuntu3.7 \
     -y 
 
 apt-get clean && \

docker/scripts/install_switchError.sh

@@ -3,7 +3,7 @@ set -euo pipefail
 
 apt-get update && apt-get install --no-install-recommends \
     r-mathlib=4.3.3-2build2 \
-    libboost-iostreams1.83-dev=1.83.0-2.1ubuntu3.1 \
+    libboost-iostreams1.83-dev=1.83.0-2.1ubuntu3.2 \
     -y && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*

tests/extras/r.R

@@ -106,6 +106,7 @@ libraries_to_check <- c(
     "gplots",
     "gridExtra",
     "Gsens",
+    "gsmr2",
     "gwasglue",
     "gwasglue2",
     "gwasurvivr",
@@ -126,12 +127,15 @@ libraries_to_check <- c(
     "lubridate",
     "kinship2",
     "MASS",
+    "matlab",
+    "matlab2r",
     "MatrixEQTL",
     "matrixStats",
     "MendelianRandomization",
     "mgcv",
     "miniCRAN",
     "MRBEE",
+    "MRlap",
     "MVMR",
     "modelr",
     "moments",
@@ -150,6 +154,10 @@ libraries_to_check <- c(
     "pracma",
     "PredictABEL",
     "psych",
+    "raveio",
+    "rhdf5",
+    "R.matlab",
+    "rmatio",
     "RColorBrewer",
     "Rcpp",
     "readxl",
@@ -177,6 +185,7 @@ libraries_to_check <- c(
     "tree",
     "viridis")
 
+
 # Define a test
 test_that("Required libraries are installed", {
   missing_libraries <- setdiff(libraries_to_check, installed.packages()[, "Package"])