I have cat orthomcl/Dockerfile:
FROM debian:stretch-backports
RUN apt-get update && apt-get install -y --no-install-recommends \
wget \
cpanminus \
build-essential \
default-libmysqlclient-dev \
python \
ca-certificates \
&& rm -rf /var/lib/apt/lists/*
RUN mkdir diamond \
&& cd diamond \
&& wget -c https://github.com/bbuchfink/diamond/releases/download/v0.9.14/diamond-linux64.tar.gz \
&& tar xvf diamond-linux64.tar.gz \
&& rm *.tar.gz
RUN cpanm DBI DBD::mysql
RUN wget -c https://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 -c https://orthomcl.org/common/downloads/software/v2.0/orthomclSoftware-v2.0.9.tar.gz
RUN tar xvf orthomclSoftware-v2.0.9.tar.gz
ENV PATH="/diamond:/orthomclSoftware-v2.0.9/bin:${PATH}"
This is my docker-compose.yml:
orthomcl:
tty: true
build: orthomcl
restart: always
links:
- db
volumes:
- ./output_dir/:/output_dir
db:
image: mysql
restart: always
environment:
- MYSQL_ROOT_PASSWORD=PAssw0rd
ports:
- "3306:3306"
volumes:
- ./mysql/:/docker-entrypoint-initdb.d
Next, I used docker-compose up which caused:
db_1 | 2019-05-02T23:59:03.981494Z 0 [Warning] [MY-011070] [Server] 'Disabling symbolic links using --skip-symbolic-links (or equivalent) is the default. Consider not using this option as it' is deprecated and will be removed in a future release.
db_1 | 2019-05-02T23:59:03.981697Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.16) starting as process 1
db_1 | 2019-05-02T23:59:04.113140Z 1 [System] [MY-011012] [Server] Starting upgrade of data directory.
db_1 | 2019-05-02T23:59:04.354244Z 1 [ERROR] [MY-012530] [InnoDB] Unknown redo log format (103). Please follow the instructions at http://dev.mysql.com/doc/refman/8.0/en/ upgrading-downgrading.html.
db_1 | 2019-05-02T23:59:04.354289Z 1 [ERROR] [MY-012930] [InnoDB] Plugin initialization aborted with error Generic error.
db_1 | 2019-05-02T23:59:04.862813Z 1 [ERROR] [MY-011013] [Server] Failed to initialize DD Storage Engine.
db_1 | 2019-05-02T23:59:04.863115Z 0 [ERROR] [MY-010020] [Server] Data Dictionary initialization failed.
db_1 | 2019-05-02T23:59:04.863285Z 0 [ERROR] [MY-010119] [Server] Aborting
db_1 | 2019-05-02T23:59:04.868499Z 0 [System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.16) MySQL Community Server - GPL.
db_1 | 2019-05-02T23:59:07.188586Z 0 [Warning] [MY-011070] [Server] 'Disabling symbolic links using --skip-symbolic-links (or equivalent) is the default. Consider not using this option as it' is deprecated and will be removed in a future release.
db_1 | 2019-05-02T23:59:07.188730Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.16) starting as process 1
db_1 | 2019-05-02T23:59:07.198834Z 1 [System] [MY-011012] [Server] Starting upgrade of data directory.
db_1 | 2019-05-02T23:59:07.310233Z 1 [ERROR] [MY-012530] [InnoDB] Unknown redo log format (103). Please follow the instructions at http://dev.mysql.com/doc/refman/8.0/en/ upgrading-downgrading.html.
db_1 | 2019-05-02T23:59:07.310273Z 1 [ERROR] [MY-012930] [InnoDB] Plugin initialization aborted with error Generic error.
db_1 | 2019-05-02T23:59:07.826041Z 1 [ERROR] [MY-011013] [Server] Failed to initialize DD Storage Engine.
db_1 | 2019-05-02T23:59:07.826837Z 0 [ERROR] [MY-010020] [Server] Data Dictionary initialization failed.
db_1 | 2019-05-02T23:59:07.829033Z 0 [ERROR] [MY-010119] [Server] Aborting
db_1 | 2019-05-02T23:59:07.835484Z 0 [System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.16) MySQL Community Server - GPL.
orthomcl_db_1 exited with code 1
How is it possible to solve the above InnoDB errors?
Thank you in advance.
