Merge pull request #1 from SouthernMethodistUniversity/biostats_mcgee

Biostats mcgee

biostats_mcgee/Dockerfile

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+# docker build -t biostats:latest .
+# docker build --platform linux/amd64 -t biostats:latest .
+# docker build --no-cache --progress=plain -t biostats:latest .
+# docker run --entrypoint /bin/bash -it biostats:latest
+
+FROM rocker/rstudio:4.2.2
+LABEL maintainer="Robert Kalescky <[email protected]>"
+
+ENV DEBIAN_FRONTEND noninteractive
+
+RUN apt-get update &&\
+ apt-get remove -y libcurl4 &&\
+ apt-get upgrade -y &&\
+ apt-get install -y --no-install-recommends\
+ apt-transport-https\
+ autoconf\
+ ca-certificates\
+ cmake\
+ curl\
+ default-jdk\
+ default-jre\
+ g++\
+ gcc\
+ git\
+ git-lfs\
+ gnupg\
+ libboost-all-dev\
+ libbz2-dev\
+ libcereal-dev\
+ libcurl4-openssl-dev\
+ libgff-dev\
+ libjemalloc-dev\
+ liblzma-dev\
+ libtbb-dev\
+ libz-dev\
+ make\
+ ninja-build\
+ python3-pip\
+ software-properties-common\
+ unzip\
+ wget\
+ zlib1g-dev
+
+# FastQC
+RUN git clone --depth 1 --branch v0.11.9\
+ https://github.com/s-andrews/FastQC.git /opt/FastQC &&\
+ ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc
+
+# Cutadapt (https://cutadapt.readthedocs.io)
+RUN pip3 install cutadapt
+
+# TrimGalore!
+RUN git clone --depth 1 --branch 0.6.7\
+ https://github.com/FelixKrueger/TrimGalore.git /opt/TrimGalore &&\
+ ln -s /opt/TrimGalore/trim_galore /usr/local/bin/trim_galore
+
+# STAR
+RUN git clone --depth 1 --branch 2.7.10b\
+ https://github.com/alexdobin/STAR.git /opt/STAR &&\
+ cd /opt/STAR/source &&\
+ make STAR &&\
+ mv /opt/STAR/bin/Linux_x86_64_static/STAR* /usr/local/bin/ &&\
+ rm -rf /opt/STAR
+
+# RSEM
+RUN git clone --depth 1 --branch v1.3.3\
+ https://github.com/deweylab/RSEM.git /opt/RSEM &&\
+ cd /opt/RSEM &&\
+ make -j install &&\
+ rm -rf /opt/RSEM
+
+# Install R Packages
+COPY install_packages.R /
+RUN Rscript /install_packages.R
+
+# GATK4
+RUN git clone --depth 1 --branch 4.2.6.1\
+ https://github.com/broadinstitute/gatk.git /opt/gatk &&\
+ cd /opt/gatk &&\
+ ./gradlew installAll
+
+# Salmon
+RUN git clone --depth 1 --branch v1.9.0\
+ https://github.com/COMBINE-lab/salmon.git /opt/salmon &&\
+ mkdir /opt/salmon/build &&\
+ cd /opt/salmon/build &&\
+ cmake .. &&\
+ make install
+

biostats_mcgee/biostats.lua

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+load("singularity")
+
+local img_name      = 'biostats_latest-2023-02-07-858e2914ccfc.sif'
+local img_directory = '/hpc/applications/containers/'
+local img_path      = pathJoin(img_directory, img_name)
+
+function build_command(cmd)
+  local home          = os.getenv("HOME")
+  local user_libs     = pathJoin(home, 'R/portal/rocker-images/biostats_0')
+  local cmd           = 'singularity exec --nv '
+  local cmd_beginning = cmd .. '--env R_LIBS_USER=' .. user_libs.. ' '
+  local cmd_ending    = img_path .. ' ' .. cmd
+  local sh_ending     = ' "$@"'
+  local csh_ending    = ' $*'
+  local sh_cmd        = cmd_beginning .. cmd_ending .. sh_ending
+  local csh_cmd       = cmd_beginning .. cmd_ending .. csh_ending
+  set_shell_function(cmd, sh_cmd, csh_cmd)
+end
+
+local executables = {
+  'python3'
+  'R',
+  'Rscript',
+  'rserver',
+  'rstudio-server',
+  'fastqc',
+  'cutadapt',
+  'STAR',
+  'STARlong',
+  'rsem-bam2readdepth',
+  'rsem-get-unique',
+  'rsem-run-em',
+  'rsem-bam2wig',
+  'rsem-gff3-to-gtf',
+  'rsem-run-gibbs',
+  'rsem-build-read-index',
+  'rsem-parse-alignments',
+  'rsem-sam-validator',
+  'rsem-calculate-credibility-intervals',
+  'rsem-plot-model',
+  'rsem-scan-for-paired-end-reads',
+  'rsem-calculate-expression',
+  'rsem-plot-transcript-wiggles',
+  'rsem-simulate-reads',
+  'rsem-extract-reference-transcripts',
+  'rsem-prepare-reference',
+  'rsem-synthesis-reference-transcripts',
+  'rsem-generate-data-matrix',
+  'rsem-preref',
+  'rsem-tbam2gbam',
+  'rsem-gen-transcript-plots',
+  'rsem-refseq-extract-primary-assembly' 
+}
+
+for _, executable in ipairs(executables) do
+  build_command(executable)
+end
+

biostats_mcgee/build_images.sh

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+#!/usr/bin/env zsh
+
+# Set version
+version="latest"
+
+# Set platform
+#if [ -z "$1" ]; then
+case $1 in
+m[2,3,p])
+    platform="linux/amd64"
+    ;;
+*)
+    platform="linux/$(uname -m)"
+    ;;
+esac
+
+# Build container with Docker
+docker build --platform ${platform} -t biostats:${version} .
+
+# Convert Docker image to Singularity image
+docker run -v /var/run/docker.sock:/var/run/docker.sock\
+ -v $PWD:/output --privileged -t --rm\
+ singularityware/docker2singularity biostats:${version} | tee build.log
+
+# Get Singularity image name
+simg=$(basename $(awk '/Build complete/{print $NF}' build.log) | tr -d '\b\r')
+img="${simg%.*}.sif"
+mv $simg $img
+
+# Change Singularity image permissions
+if [[ $(uname -s) == "Linux" ]]; then
+    sudo chown $USER:$USER $img
+fi
+
+# Update module file with new Singularity image name
+sed -i'' -e "s/^local img_name.*/local img_name      = \'${img}\'/g"\
+ biostats.lua
+

biostats_mcgee/install_packages.R

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+cran = list(
+  packages = c(
+    "BiocManager")
+)
+
+bioc = list(
+  packages = c(
+    "edgeR",
+    "AnnotationDbi",
+    "org.Hs.eg.db"),
+  version = "3.16"
+)
+
+install.packages(cran$packages)
+BiocManager::install(version = bioc$version)
+BiocManager::install(bioc$packages)
+