From 7c4b3288613a1b11cac174087892bcd87fa90ed3 Mon Sep 17 00:00:00 2001
From: Steve Huang <shuang@broadinstitute.org>
Date: Wed, 30 Aug 2023 13:01:59 -0400
Subject: [PATCH] a docker images to be used for creating Terra cloud
 environment

---
 terra/custom_env_docker/Dockerfile | 112 +++++++++++++++++++++++++++++
 terra/custom_env_docker/Makefile   |  12 ++++
 2 files changed, 124 insertions(+)
 create mode 100644 terra/custom_env_docker/Dockerfile
 create mode 100644 terra/custom_env_docker/Makefile

diff --git a/terra/custom_env_docker/Dockerfile b/terra/custom_env_docker/Dockerfile
new file mode 100644
index 000000000..9132001b8
--- /dev/null
+++ b/terra/custom_env_docker/Dockerfile
@@ -0,0 +1,112 @@
+############### stage 0: build samtools and bcftools from source
+FROM ubuntu:20.04
+
+ARG DEBIAN_FRONTEND=noninteractive
+ARG SAMTOOLS_VERSION=1.18
+ARG BCFTOOLS_VERSION=1.18
+RUN apt-get -qqy update --fix-missing && \
+    apt-get -qqy dist-upgrade && \
+    apt-get -qqy install --no-install-recommends \
+                 ca-certificates \
+                 libbz2-dev \
+                 libcurl4-openssl-dev \
+                 liblzma-dev \
+                 libncurses5-dev \
+                 autoconf \
+                 automake \
+                 bzip2 \
+                 gcc \
+                 make \
+                 wget \
+                 zlib1g-dev && \
+    wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
+    tar xjf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
+    cd samtools-${SAMTOOLS_VERSION} && ./configure --without-curses --enable-libcurl && make -s all all-htslib && make install install-htslib && cd - && \
+    rm -rf samtools-${SAMTOOLS_VERSION}* && \
+    wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
+    tar xjf bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \
+    cd bcftools-${BCFTOOLS_VERSION} && ./configure --without-curses && make -s && make install && cd - && \
+    rm -rf bcftools-${BCFTOOLS_VERSION}* && \
+    apt-get -qqy purge autoconf automake bzip2 gcc make wget && \
+    apt-get -qqy clean && \
+    rm -rf /tmp/* \
+           /var/tmp/* \
+           /var/cache/apt/* \
+           /var/lib/apt/lists/* \
+           /usr/share/man/?? \
+           /usr/share/man/??_* && \
+    samtools --help && \
+    bcftools --help
+
+############### stage 1: other commonly used bioinformatics utilities
+FROM us.gcr.io/broad-dsde-methods/terra-jupyter-minimal-base:0.0.1
+
+USER root
+
+# copy from previous stage the binaries from samtools build
+COPY --from=0 /usr/local/bin/* /usr/local/bin/
+
+ARG lrmaCU="https://github.com/broadinstitute/lrma-cloud-utils.git"
+ARG MINIMAP2_VERSION='2.26'
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get -qqy update --fix-missing && \
+    apt-get -qqy dist-upgrade && \
+    apt-get -qqy install --no-install-recommends \
+                apt-transport-https \
+                ca-certificates \
+                gnupg \
+                zlib1g-dev \
+                aria2 \
+                bc \
+                bedtools \
+                bzip2 \
+                cron \
+                curl \
+                datamash \
+                gawk \
+                less \
+                python3.10 \
+                python3-pip \
+                tabix \
+                tmux \
+                tree \
+                vcftools \
+                wget && \
+    gcloud components update --quiet && \
+    cd /tmp && \
+    curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VERSION}/minimap2-${MINIMAP2_VERSION}_x64-linux.tar.bz2 | tar -jxvf - && \
+    cd minimap2-${MINIMAP2_VERSION}_x64-linux && \
+    mv k8 minimap2 paftools.js /usr/local/bin/ && \
+    apt-get -qqy clean && \
+    rm -rf /tmp/* \
+        /var/tmp/* \
+        /var/cache/apt/*
+
+# key library
+RUN python3 -m pip install --upgrade pip setuptools ipynbname && \
+    python3 -m pip install --upgrade \
+    git+${lrmaCU}
+
+# terminal-customization
+RUN cd /home/jupyter/ && \
+    git clone \
+        --depth=1 \
+        https://github.com/Bash-it/bash-it.git /home/jupyter/.bash_it && \
+    cd /home/jupyter/.bash_it && \
+    bash install.sh --silent && \
+    cd -
+
+# cron-related
+RUN echo 'jupyter' >> /etc/cron.allow && \
+    echo 'jupyter' >> /etc/at.allow && \
+    chmod u+s /usr/sbin/cron
+
+# sendgrid for email notification
+RUN apt-get -qqy update --fix-missing && \
+    apt-get -qqy dist-upgrade && \
+    apt-get -qqy install --no-install-recommends \
+                        postfix libsasl2-modules mailutils && \
+    apt-get -qqy clean && \
+    rm -rf /tmp/* \
+        /var/tmp/* \
+        /var/cache/apt/*
diff --git a/terra/custom_env_docker/Makefile b/terra/custom_env_docker/Makefile
new file mode 100644
index 000000000..5dd8cca3f
--- /dev/null
+++ b/terra/custom_env_docker/Makefile
@@ -0,0 +1,12 @@
+VERSION = 0.0.1
+TAG1 = us.gcr.io/broad-dsp-lrma/lr-terra-base:$(VERSION)
+TAG2 = us.gcr.io/broad-dsp-lrma/lr-terra-base:latest
+
+all: build push
+
+build:
+	docker build -t $(TAG1) -t $(TAG2) .
+
+push:
+	docker push $(TAG1)
+	docker push $(TAG2)