The idea of this repository is to create Docker containers for bioinformatics 'a la carte' using a simple Makefile that is used as a recipe to install softwares and their depedencies.
Here the make file recipes.mk contains the recipes to build a few common softwares used in bioinformatics.
But instead of using the usual SHELL=sh we use a short script make/docker.run that is going to echo the command with a prefix RUN .
For example if we want to build a docker container with samtools and bcftools, we can invoke make the following way:
$ make -f make/recipes.mk HTS_VERSION=1.20 samtools.src bcftools.src the graph of dependencies is the following one (to compile bcftools we need wget , to get wget we need to run apt-get , etc...)
┌──────┐
┌─────────────────────────────────────────────────────────────────────────────────────────────────── │ wget │ ◀┐
│ └──────┘ │
│ │
│ ┌────────────────────────────────────────────────────────────────────────────┐ │
│ │ │ │
│ │ ┌───────────────────┐ │ ┌──────────────┐ │
│ │ │ dockerfile.header │ │ │ bzip2 │ ─────────┼──────────────────────────────────────┐
│ │ └───────────────────┘ │ └──────────────┘ │ │
│ │ │ │ ▲ │ │
│ │ │ │ │ │ │
│ ▼ ▼ │ │ │ │
│ ┌────────────────────┐ ┌──────────────────────┐ ┌───────────────────────────────────────────────────────────────┐ ┌─────────────────┐ │
│ │ python3-matplotlib │ │ libcurl4-openssl-dev │ ◀── │ │ ──▶ │ libncurses5-dev │ │
│ └────────────────────┘ └──────────────────────┘ │ │ └─────────────────┘ │
│ │ │ │ │ │ │
│ │ │ │ apt.get.update │ │ │
│ │ │ │ │ │ │
│ │ │ │ │ │ │
│ │ │ ┌─ │ │ ─┐ │ │
│ │ │ │ └───────────────────────────────────────────────────────────────┘ │ │ │
│ │ │ │ │ │ │ │ │ │
│ │ │ │ │ │ │ │ │ │
│ │ │ │ ▼ ▼ ▼ │ │ │
│ │ │ │ ┌───────────────────┐ ┌──────────────┐ ┌─────────────┐ │ │ │
│ │ │ │ │ libbz2-dev │ │ g │ │ liblzma-dev │ │ │ │
│ │ │ │ └───────────────────┘ └──────────────┘ └─────────────┘ │ │ │
│ │ │ │ │ │ │ │ │ │
│ │ ┌────┼───────────────────────┘ │ │ │ │ │ │
│ │ │ │ ▼ ▼ │ │ │ │
│ │ │ │ ┌────────────────────────────────────────┐ │ │ │ │
│ │ │ └────────────────────────▶ │ │ ◀────────┘ │ │ │
│ │ │ │ │ │ │ │
│ │ │ │ │ │ │ │
│ │ │ │ common.c.compile │ ◀───────────────────────┼────┘ │
│ │ │ │ │ │ │
│ │ │ ┌──────────────────────┐ │ │ │ │
│ │ └▶ │ make │ ──▶ │ │ ◀────────┐ │ │
│ │ └──────────────────────┘ └────────────────────────────────────────┘ │ │ │
│ │ │ │ │ │
│ │ │ │ │ │
│ │ ▼ │ │ │
│ │ ┌────────────────────────────────────────┐ │ │ │
│ │ │ htslib.src │ ◀────────┼──────────────┼───────────────────────┘
│ │ └────────────────────────────────────────┘ │ │
│ │ │ ▲ │ │ │
│ │ │ │ │ │ │
│ │ ▼ │ ▼ │ │
│ │ ┌───────────────────┐ │ ┌──────────────┐ │ │
│ └───────────────────────────────────────────────────▶ │ bcftools.src │ │ │ samtools.src │ │ │
│ └───────────────────┘ │ └──────────────┘ │ │
│ │ │ │
└─────────────────────────────────────────────────────────────────────────────────┘ │ │
│ │
┌───────────────────┐ │ │
│ libz-dev │ ──────────────────────────────┘ │
└───────────────────┘ │
▲ │
└────────────────────────────────────────────────────────────────┘
'make' prints
FROM ubuntu:22.04
# update apt
RUN apt-get -y update
RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install wget
RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install make
RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install libz-dev
RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install libbz2-dev
RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install g++
RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install liblzma-dev
RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install libcurl4-openssl-dev
RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install libncurses5-dev
RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install bzip2
RUN cd /opt/ && \
wget -O htslib-1.20.tar.bz2 "https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2" && \
tar xvfj htslib-1.20.tar.bz2 && \
cd htslib-1.20 && \
make && \
rm ../htslib-1.20.tar.bz2
ENV PATH=/opt/htslib-1.20:${PATH}
RUN cd /opt/ && \
wget -O samtools-1.20.tar.bz2 "https://github.com/samtools/samtools/releases/download/1.20/samtools-1.20.tar.bz2" && \
tar xvfj samtools-1.20.tar.bz2 && \
cd samtools-1.20 && \
make HTSDIR=/opt/htslib-1.20 && \
rm ../samtools-1.20.tar.bz2
ENV PATH=/opt/samtools-1.20:${PATH}
RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install python3-matplotlib
RUN cd /opt/ && \
wget -O bcftools-1.20.tar.bz2 "https://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2" && \
tar xvfj bcftools-1.20.tar.bz2 && \
cd bcftools-1.20 && \
make HTSDIR=/opt/htslib-1.20 && \
rm ../bcftools-1.20.tar.bz2
ENV PATH=/opt/bcftools-1.20:${PATH}
ENV BCFTOOLS_PLUGINS=/opt/bcftools-1.20/pluginsand this output can be piped into docker build
make -f make/recipes.mk HTS_VERSION=1.20 samtools.src bcftools.src |\
BUILDKIT_PROGRESS=plain docker build -t bioinfo1 -
#1 [internal] load .dockerignore
#1 transferring context: 2B done
#1 DONE 0.6s
(...)
#5 [ 1/15] FROM docker.io/library/ubuntu:22.04@sha256:1b8d8ff4777f36f19bfe73ee4df61e3a0b789caeff29caa019539ec7c9a57f95
#6 [ 2/15] RUN apt-get -y update
#7 [ 3/15] RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install wget
#8 [ 4/15] RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install make
#9 [ 5/15] RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install libz-dev
#10 [ 6/15] RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install libbz2-dev
#11 [ 7/15] RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install g++
#12 [ 8/15] RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install liblzma-dev
#13 [ 9/15] RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install libcurl4-openssl-dev
#14 [10/15] RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install libncurses5-dev
#15 [11/15] RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install bzip2
#16 [12/15] RUN cd /opt/ && wget -O htslib-1.20.tar.bz2 "https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2" && tar xvfj htslib-1.20.tar.bz2 && cd htslib-1.20 && make && rm ../htslib-1.20.tar.bz2
#16 1.275 --2024-04-19 12:20:00-- https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2
#17 [13/15] RUN cd /opt/ && wget -O samtools-1.20.tar.bz2 "https://github.com/samtools/samtools/releases/download/1.20/samtools-1.20.tar.bz2" && tar xvfj samtools-1.20.tar.bz2 && cd samtools-1.20 && make HTSDIR=/opt/htslib-1.20 && rm ../samtools-1.20.tar.bz2
(...)
#20 exporting to image
#20 exporting layers
#20 exporting layers 30.4s done
#20 writing image sha256:8ad7f204b6cf3af52764993fa94c5249af1b0d635c3de05932cec260cbe65257 0.0s done
#20 naming to docker.io/library/bioinfo1
#20 naming to docker.io/library/bioinfo1 0.1s done
#20 DONE 30.5sAnother example:
make -nBd -f make/recipes.mk r.ggplot2 bwa.src gatk4.github jvarkit.github samtools.src bcftools.src jvarkit.github 
Pierre Lindenbaum PhD. Institut du Thorax. Nantes. France
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent