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Merge pull request #108 from LCR-BCCRC/houman_dev
WGCNA and DriveMuTR dockerfiles
2 parents d2cbb38 + 2c69db4 commit 3245626

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‎cnaqc/1.0/Dockerfile‎

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@@ -42,6 +42,7 @@ RUN mamba install --yes --name base \
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openssl \
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libxml2 \
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libgit2 \
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jq \
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&& rm -rf /opt/conda/pkgs/*
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RUN R --vanilla -q -e 'remotes::install_github("caravagnalab/CNAqc", lib="/opt/conda/lib/R/library", dependencies = TRUE, upgrade = "never")'

‎drivemutr/1.0/Dockerfile‎

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FROM mambaorg/micromamba:2.8.1
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LABEL org.opencontainers.image.source="https://github.com/LCR-BCCRC/lcr-scripts"
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ENV LC_ALL=C.UTF-8
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ENV LANG=C.UTF-8
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RUN micromamba install --yes --name base \
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--channel conda-forge \
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--channel bioconda \
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--strict-channel-priority \
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r-base=4.4 \
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r-tidyverse \
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r-broom \
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r-ggbeeswarm \
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r-iml \
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r-pre \
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r-remotes \
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r-rlang \
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r-biocmanager \
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r-devtools \
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r-dt \
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bioconductor-variantannotation \
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bioconductor-motifstack \
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bioconductor-gviz \
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bioconductor-biocparallel=1.40.0 \
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bioconductor-biostrings=2.74.0 \
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bioconductor-bsgenome.hsapiens.ucsc.hg19=1.4.3 \
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bioconductor-genomicranges \
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bioconductor-iranges \
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bioconductor-motifdb \
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bioconductor-rtracklayer \
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git \
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jq \
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make \
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c-compiler \
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cxx-compiler \
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fortran-compiler \
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pkg-config \
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&& micromamba clean --all --yes
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RUN micromamba run --name base R --vanilla -q -e 'devtools::install_github( \
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"Simon-Coetzee/motifBreakR", \
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dependencies = NA, \
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upgrade = "never" \
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)'
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RUN micromamba run --name base R --vanilla -q -e 'options(timeout = 3600); devtools::install_github( \
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"morinlab/GAMBLR.data", \
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dependencies = FALSE, \
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upgrade = "never" \
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)'
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CMD ["/bin/bash"]

‎drivemutr/1.0/run_tests.sh‎

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#!/usr/bin/env bash
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# Smoke tests for the DriveMuTR container.
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# Verifies that all required tools and R packages are present and loadable.
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# Usage: ./run_tests.sh
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PASS=true
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check() {
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local desc="$1"
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local cmd="$2"
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local output
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output=$(eval "$cmd" 2>&1)
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if [ $? -eq 0 ]; then
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echo "PASS: $desc"
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else
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echo "FAIL: $desc"
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echo "$output" | sed 's/^/ /'
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PASS=false
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fi
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}
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check "Rscript is available" "command -v Rscript"
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check "R package dplyr loads" "Rscript --vanilla -e 'library(dplyr)'"
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check "R package tidyr loads" "Rscript --vanilla -e 'library(tidyr)'"
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check "R package tibble loads" "Rscript --vanilla -e 'library(tibble)'"
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check "R package purrr loads" "Rscript --vanilla -e 'library(purrr)'"
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check "R package readr loads" "Rscript --vanilla -e 'library(readr)'"
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check "R package stringr loads" "Rscript --vanilla -e 'library(stringr)'"
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check "R package ggplot2 loads" "Rscript --vanilla -e 'library(ggplot2)'"
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check "R package rlang loads" "Rscript --vanilla -e 'library(rlang)'"
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check "R package broom loads" "Rscript --vanilla -e 'library(broom)'"
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check "R package ggbeeswarm loads" "Rscript --vanilla -e 'library(ggbeeswarm)'"
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check "R package iml loads" "Rscript --vanilla -e 'library(iml)'"
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check "R package pre loads" "Rscript --vanilla -e 'library(pre)'"
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check "R package BiocParallel loads" "Rscript --vanilla -e 'library(BiocParallel)'"
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check "R package Biostrings loads" "Rscript --vanilla -e 'library(Biostrings)'"
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check "R package GenomicRanges loads" "Rscript --vanilla -e 'library(GenomicRanges)'"
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check "R package IRanges loads" "Rscript --vanilla -e 'library(IRanges)'"
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check "R package rtracklayer loads" "Rscript --vanilla -e 'library(rtracklayer)'"
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check "R package MotifDb loads" "Rscript --vanilla -e 'library(MotifDb)'"
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check "R package motifbreakR loads" "Rscript --vanilla -e 'library(motifbreakR)'"
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check "R package BSgenome.Hsapiens.UCSC.hg19 loads" "Rscript --vanilla -e 'library(BSgenome.Hsapiens.UCSC.hg19)'"
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check "R package GAMBLR.data loads" "Rscript --vanilla -e 'library(GAMBLR.data)'"
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$PASS

‎igseqr/1.0.1/Dockerfile‎

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"samtools=1.16.1" \
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"trinity=2.13.2" \
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"git" \
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"jq" \
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&& mamba clean --all --yes \
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&& /opt/conda/envs/env/bin/git clone --branch v1.0.1 --depth 1 \
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https://github.com/ForconiLab/IgSeqR.git /tmp/IgSeqR \

‎wgcna/1.73/Dockerfile‎

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FROM mambaorg/micromamba:2.8.1
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LABEL org.opencontainers.image.source="https://github.com/LCR-BCCRC/lcr-scripts"
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ENV LC_ALL=C.UTF-8
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ENV LANG=C.UTF-8
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RUN micromamba install --yes --name base \
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--channel conda-forge \
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--channel bioconda \
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--strict-channel-priority \
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r-base=4.4 \
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r-tidyverse \
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r-matrixstats \
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r-remotes \
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r-config \
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r-ggthemes \
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r-magrittr \
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r-stringr \
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bioconductor-deseq2=1.46.0 \
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bioconductor-limma \
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bioconductor-biocparallel=1.40.0 \
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r-wgcna=1.73 \
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git \
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jq \
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make \
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c-compiler \
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cxx-compiler \
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fortran-compiler \
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pkg-config \
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&& micromamba clean --all --yes
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RUN micromamba run --name base R --vanilla -q -e 'remotes::install_github("morinlab/GAMBLR.helpers@fdde14c", lib="/opt/conda/lib/R/library", dependencies = TRUE, upgrade = "never")'
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CMD ["/bin/bash"]

‎wgcna/1.73/run_tests.sh‎

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#!/usr/bin/env bash
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# Smoke tests for the WGCNA container.
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# Verifies that all required tools and R packages are present and loadable.
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# Usage: ./run_tests.sh
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PASS=true
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check() {
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local desc="$1"
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local cmd="$2"
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local output
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output=$(eval "$cmd" 2>&1)
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if [ $? -eq 0 ]; then
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echo "PASS: $desc"
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else
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echo "FAIL: $desc"
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echo "$output" | sed 's/^/ /'
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PASS=false
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fi
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}
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check "Rscript is available" "command -v Rscript"
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check "R package dplyr loads" "Rscript --vanilla -e 'library(dplyr)'"
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check "R package tidyr loads" "Rscript --vanilla -e 'library(tidyr)'"
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check "R package tibble loads" "Rscript --vanilla -e 'library(tibble)'"
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check "R package readr loads" "Rscript --vanilla -e 'library(readr)'"
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check "R package ggplot2 loads" "Rscript --vanilla -e 'library(ggplot2)'"
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check "R package matrixStats loads" "Rscript --vanilla -e 'library(matrixStats)'"
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check "R package DESeq2 loads" "Rscript --vanilla -e 'library(DESeq2)'"
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check "R package limma loads" "Rscript --vanilla -e 'library(limma)'"
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check "R package BiocParallel loads" "Rscript --vanilla -e 'library(BiocParallel)'"
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check "R package WGCNA loads" "Rscript --vanilla -e 'library(WGCNA)'"
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check "R package GAMBLR.helpers loads" "Rscript --vanilla -e 'library(GAMBLR.helpers)'"
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$PASS

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