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a docker image to be used for creating Terra cloud environment #421

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112 changes: 112 additions & 0 deletions terra/custom_env_docker/Dockerfile
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############### 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/*
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What about other common cloud utilities, such as gsutil? Does the terra base image include that?

FYI, this is how I usually install it so crcmod works and parallel uploads/downloads are fast:

# install gsutil
RUN apt-get --allow-releaseinfo-change update
RUN apt install -y curl git-lfs time datamash
RUN curl https://sdk.cloud.google.com | bash

# Setup crcmodc for gsutil:
RUN apt-get install -y gcc python3-dev python3-setuptools && \
			pip3 uninstall -y crcmod && \
			pip3 install --no-cache-dir -U crcmod

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yes, you're right. The base image I depend on handles the google cloud stuff.
I don't want to mess with that, other than that line which updates the google cloud cli.

12 changes: 12 additions & 0 deletions terra/custom_env_docker/Makefile
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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)