QTL-seq pipeline に必要なツール群

Dockerfile

###
#
# QTL-seq pipline
# see also: http://genome-e.ibrc.or.jp/home/bioinformatics-team/mutmap/QTL-seq_quick_start_guide_brief_Rev0.0.pdf
#
# Usage:
# 0. change directory to the working directory
# 1. curl -O -L https://gist.githubusercontent.com/duck8823/3ef65d29328b2f99057d5f67dbc86e24/raw/Dockerfile
# 2. docker build -t qtl_seq .
# 3. curl -O -L http://genome-e.ibrc.or.jp/home/bioinformatics-team/mutmap/QTL-seq_framework1.4.4.tar.gz
# 4. tar xzvf QTL-seq_framework1.4.4.tar.gz -C ./
# 5. docker run -it -v $PWD/QTL-seq_framework1.4.4:/workspace qtl_seq bash
# -. Fun pipiline!
#
###

# 1. perl 5.8.8 (イメージは5.8.9
FROM perl:5.8

WORKDIR /tmp/

# 2. Perl module Math::Random::MT::Auto 6.14
RUN cpanm Math::Random::MT::Auto@6.14

# 3. R (version 2.15.0)
## Fortrun77コンパイラのインストールに必要なリポジトリを追加
RUN echo "deb [trusted=yes] http://old-releases.ubuntu.com/ubuntu/ hardy universe" >> /etc/apt/sources.list \
 && echo "deb-src [trusted=yes] http://old-releases.ubuntu.com/ubuntu/ hardy universe" >> /etc/apt/sources.list \
 && echo "deb [trusted=yes] http://old-releases.ubuntu.com/ubuntu/ hardy-updates universe" >> /etc/apt/sources.list \
 && echo "deb-src [trusted=yes] http://old-releases.ubuntu.com/ubuntu/ hardy-updates universe" >> /etc/apt/sources.list

## Fortrun77コンパイラのインストール
RUN apt update \
 && apt install -y g77
## R のインストール
RUN curl http://cran.r-project.org/src/base/R-2/R-2.15.0.tar.gz | tar xz -C /tmp/
WORKDIR /tmp/R-2.15.0
RUN ./configure \
 && make \
 && make install

WORKDIR /tmp/

# 4. BWA (version 0.5.9-r16)
RUN curl -O -L http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2 \
 && tar xjvf bwa-0.5.9.tar.bz2 -C /usr/local/src/
WORKDIR /usr/local/src/bwa-0.5.9
RUN make \
 && ln -s /usr/local/src/bwa-0.5.9/bwa /usr/local/bin/bwa

WORKDIR /tmp/

# 5. SAMtools (0.1.8 or before)
RUN curl -O -L http://sourceforge.net/projects/samtools/files/samtools/0.1.8/samtools-0.1.8.tar.bz2 \
 && tar xjvf samtools-0.1.8.tar.bz2 -C /usr/local/src/
WORKDIR /usr/local/src/samtools-0.1.8
RUN make \
 && ln -s /usr/local/src/samtools-0.1.8/samtools /usr/local/bin/samtools

WORKDIR /tmp/

# 6. FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
## precompiled binary を使う
RUN mkdir /usr/local/fastx_toolkit_0.0.13
RUN curl -O -L http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2 \
 && tar xjvf fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2 -C /usr/local/fastx_toolkit_0.0.13

ENV PATH=$PATH:/usr/local/fastx_toolkit_0.0.13/bin

# その他
## スクリプト で /bin/sh が指定されているので /bin/bash で実行されるようにする
RUN mv /bin/sh /bin/sh.bk \
 && ln -s /bin/bash /bin/sh

## スクリプト で /usr/bin/perl が指定されているので /usr/local/bin/perl で実行されるようにする
RUN mv /usr/bin/perl /usr/bin/perl.bk \
 && ln -s /usr/local/bin/perl /usr/bin/perl

## エディタ
RUN apt install -y vim
RUN echo "syntax on" >> ~/.vimrc
RUN echo "set number" >> ~/.vimrc

## ターミナル
RUN echo "export PS1='\[\033[40;1;32m\]\h:\w \[\033[40;2;37m\]\t\[\033[0m\] \n$ '" >> ~/.bashrc

# Install QTL-seq pipline
RUN curl -O -L http://genome-e.ibrc.or.jp/home/bioinformatics-team/mutmap/QTL-seq_framework1.4.4.tar.gz \
 && tar xzvf QTL-seq_framework1.4.4.tar.gz -C /tmp/
RUN mv /tmp/QTL-seq_framework1.4.4 /workspace

WORKDIR /workspace/

/usr/local/bin/perl => /usr/bin/perl
/bin/bash => /bin/sh

やっとく必要ありそう。