Add Python environment (#11)

* Add Python env
Fixes #10

.github/workflows/docker.yml

@@ -8,9 +8,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: hadolint
         uses: reviewdog/action-hadolint@v1
         with:
           reporter: github-pr-review # Default is github-pr-check
           fail_on_error: true
+          hadolint_ignore: SC2086

.github/workflows/python.yml

@@ -8,9 +8,9 @@ jobs:
     name: Lint
     steps:
       - name: Check out source repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Python environment
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: flake8 Lint

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - Added Docker build push action to push images to GH container registry
+- Added Python environment with basic dependencies for MiX3R (jupyter, numpy, pandas, scipy, matplotlib, numba, ++)
 
 ### Updated
 

docker/dockerfiles/ldpred2/Dockerfile

@@ -16,6 +16,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     update-ca-certificates
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
+    bzip2=1.0.8-5build1 \
     cmake=3.22.1-1ubuntu1.22.04.2 \
     curl=7.81.0-1ubuntu1.16 \
     libatlas-base-dev=3.10.3-12ubuntu1 \
@@ -27,18 +28,17 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     node-shasum=1.0.2-3 \
     patch=2.7.6-7build2 \
     unzip=6.0-26ubuntu3.2 \
-    wget=1.21.2-2ubuntu1 \
     zlib1g-dev=1:1.2.11.dfsg-2ubuntu9.2 \
     && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
 # R dependencies
-RUN R -e "install.packages(c('devtools', 'argparser', 'bigsnpr', 'data.table', 'optparse', 'stringr', 'R.utils', 'tidyverse'), dependencies=c('Depends', 'Imports', 'LinkingTo'))"
+RUN R -e "install.packages(c('devtools', 'argparser', 'bigsnpr', 'data.table', 'essentials', 'eulerr', 'IRkernel', 'optparse', 'stringr', 'R.utils', 'tidyverse'), dependencies=c('Depends', 'Imports', 'LinkingTo'))"
 
 
 # install plink 1.9
-RUN wget -q --no-check-certificate https://github.com/chrchang/plink-ng/archive/refs/tags/v2.00a4.5.zip && \
+RUN curl -sSL https://github.com/chrchang/plink-ng/archive/refs/tags/v2.00a4.5.zip -o v2.00a4.5.zip && \
     unzip v2.00a4.5.zip
 
 WORKDIR /tmp/plink-ng-2.00a4.5/1.9
@@ -56,7 +56,7 @@ RUN rm -rf v2.00a4.5.zip plink-ng-2.00a4.5
 
 # install PRSice-2
 COPY patches/*.diff /tmp/patches/
-RUN wget -q --no-check-certificate https://github.com/choishingwan/PRSice/archive/refs/tags/2.3.5.zip && \
+RUN curl -sSL https://github.com/choishingwan/PRSice/archive/refs/tags/2.3.5.zip -o 2.3.5.zip && \
     unzip 2.3.5.zip
 
 WORKDIR /tmp/PRSice-2.3.5
@@ -78,7 +78,29 @@ RUN cmake ../ && \
 WORKDIR /tmp 
 RUN rm -rf 2.3.5.zip PRSice-2.3.5
 
+WORKDIR /tmp/miniforge
+RUN curl -sSL "https://github.com/conda-forge/miniforge/releases/download/24.3.0-0/Miniforge3-24.3.0-0-$("uname")-$("uname" "-m").sh" -o /tmp/miniforge.sh \
+    && mkdir /root/.conda \
+    && bash /tmp/miniforge.sh -bfp /usr/local \
+    && rm -rf /tmp/miniforge.sh \
+    && export PATH=$PATH:/opt/conda/bin
+
+RUN mamba install \
+    python=3.11 \
+    conda-pack==0.7.1 \
+    numpy==1.26.4 \
+    scipy==1.13.0 \
+    numba==0.59.1 \
+    pandas==2.2.2 \
+    matplotlib-base==3.8.4 \
+    seaborn==0.13.2 \
+    notebook==7.1.3 \
+    --yes && \
+    mamba install icc_rt==2020.2 --channel numba --yes
+
 # clean up
-RUN rm -rf /tmp/*
+RUN mamba clean -a -y && \
+        pip cache purge && \
+    rm -rf /tmp/*
 
-WORKDIR /
+WORKDIR /

scripts/LDpred2/run_ldpred2_w_docker.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+# pull docker image and tag it as "ldpred2:latest"
+docker pull --platform=linux/amd64 ghcr.io/comorment/ldpred2:latest
+docker image tag ghcr.io/comorment/ldpred2:latest ldpred2:latest
+
+bash  # make sure you run bash locally, not zsh (which is the default shell in some systems - e.g. macOS)
+
+# input/output files
+export fileGeno=/REF/examples/prsice2/EUR.bed
+export fileGenoRDS=EUR.rds
+export fileSumstats=/REF/examples/prsice2/Height.gwas.txt.gz
+export fileOut=Height
+
+# set environmental variables. Replace $REPOS with 
+# the full path to the folder containing cloned "containers" and "ldpred2_ref" repositories
+export REPOS=~/Repositories
+export REFERENCE=$REPOS/containers/reference  # clone of https://github.com/comorment/containers
+export LDPRED2_REF=$REPOS/ldpred2_ref  # clone of https://github.com/comorment/ldpred2_ref
+export CONTAINER="ldpred2:latest"
+export RSCRIPT="docker run --platform=linux/amd64 --mount type=bind,source=${PWD},target=/home --mount type=bind,source=${REFERENCE},target=/REF --mount type=bind,source=${LDPRED2_REF},target=/ldpred2_ref -w=/home/ ${CONTAINER} Rscript"
+
+# run tasks
+# $RSCRIPT /home/createBackingFile.R --file-input $fileGeno --file-output /home/$fileGenoRDS
+$RSCRIPT createBackingFile.R --file-input $fileGeno --file-output $fileGenoRDS
+
+# impute
+$RSCRIPT imputeGenotypes.R --impute-simple mean0 --geno-file-rds $fileGenoRDS
+
+# Generate PGS using LDPRED2-auto
+$RSCRIPT ldpred2.R \
+ --ldpred-mode auto \
+ --col-stat OR \
+ --col-stat-se SE \
+ --stat-type OR \
+ --geno-file-rds $fileGenoRDS \
+ --sumstats $fileSumstats \
+ --out $fileOut.auto
+

tests/extras/r.R

@@ -11,8 +11,11 @@ libraries_to_check <- c(
     "devtools",
     "data.table",
     "dplyr",
+    "essentials",
+    "eulerr",
     "ggplot2",
     "grDevices",
+    "IRkernel",
     "methods",
     "optparse",
     "R.utils",

tests/test_ldpred2_standalone.py

@@ -67,6 +67,22 @@ def test_ldpred2_R_packages():
     assert out.returncode == 0
 
 
+def test_ldpred2_python3_packages():
+    packages = [
+        'notebook',
+        'numba',
+        'numpy',
+        'matplotlib',
+        'pandas',
+        'scipy',
+        'seaborn',
+    ]
+    for pkg in packages:
+        call = f'{PREFIX} python3 -c "import {pkg}"'
+        out = subprocess.run(call, shell=True, check=True)
+        assert out.returncode == 0
+
+
 def test_ldpred2_bin_prsice():
     call = f'{PREFIX} PRSice --version'
     out = subprocess.run(call.split(' '), check=True)