I have cat orthomcl/Dockerfile
:
FROM debian:stretch-backports
RUN apt-get update && apt-get install -y --no-install-recommends \
wget \
cpanminus \
build-essential \
libmariadbclient-dev \
python \
ca-certificates \
&& rm -rf /var/lib/apt/lists/*
RUN wget http://www.micans.org/mcl/src/mcl-latest.tar.gz
RUN tar xvf mcl-latest.tar.gz
RUN cd mcl-* && ./configure && make && make install
RUN wget https://orthomcl.org/common/downloads/software/v2.0/orthomclSoftware-v2.0.9.tar.gz
RUN tar xvf orthomclSoftware-v2.0.9.tar.gz
RUN cpanm DBI DBD::mysql
RUN mkdir diamond \
&& cd diamond \
&& wget http://github.com/bbuchfink/diamond/releases/download/v0.9.14/diamond-linux64.tar.gz \
&& tar xvf diamond-linux64.tar.gz \
&& rm *.tar.gz
#COPY my.cnf /etc/mysql/
#COPY run_orthomcl.py /bin/
ENV PATH="/diamond:/orthomclSoftware-v2.0.9/bin:${PATH}"
This is my docker-compose.yml
:
orthomcl:
build: orthomcl
restart: always
links:
- db
volumes:
- ./output_dir/:/output_dir
db:
image: mariadb
restart: always
environment:
- MYSQL_ROOT_PASSWORD=PAssw0rd
ports:
- "3306:3306"
volumes:
- ./mysql/:/docker-entrypoint-initdb.d
Unfortunately, docker-compose up
caused the below error:
Starting orthomcl_db_1 ... done
Starting orthomcl_orthomcl_1 ... done
Attaching to orthomcl_db_1, orthomcl_orthomcl_1
...
db_1 | 2019-05-02 11:31:05 0 [Note] mysqld: ready for connections.
db_1 | Version: '10.3.14-MariaDB-1:10.3.14+maria~bionic' socket: '/var/run/mysqld/mysqld.sock' port: 3306 mariadb.org binary distribution
orthomcl_orthomcl_1 exited with code 0
orthomcl_orthomcl_1 exited with code 0
What did I miss?