mysql和ORTHOMCL_OrthoMCL 安装配置与使用

1. mysql安装配置(点我)

2. 创建数据库和数据库用户

2.1 以root身份登陆mysql server

./bin/mysql --defaults-file=mysql.cnf -u root -p

2.2 创建数据库和用户

CREATE DATABASE orthomcl; #建数据库

GRANT SELECT,INSERT,UPDATE,DELETE,CREATE VIEW,CREATE, INDEX, DROP on orthomcl.* TO orthomcl@localhost; #授权

set password for orthomcl@localhost = password('123456');

3. 为mysql安装perl依赖包

3.1 检查依赖包是否安装(不报错说明已经安装，反之报错)

$ perl -MDBI -e 1 (我的不报错说明已安装)

$ perl -MDBD::mysql -e 1 (报错，需要安装，见步骤3.2)

3.2 以root身份安装，没有root见3.2s

perl -MCPAN -e shell

cpan> o conf makepl_arg "mysql_config=/share/soft/mysql/bin/mysql_config"

cpan> install Data::Dumper

cpan> install DBI

cpan> force install DBD::mysql

若遇到：“ install_driver(mysql) failed: Can’t load ‘/usr/local/lib64/perl5/auto/DBD/mysql/mysql.so’ for module DBD::mysql: libmysqlclient.so.18: ” 类似的错误，把libmysqlclient.so.18所在目录的路径名加到“/etc/ld.so.conf”文件中,接着运行ldconfig即可(详情点我)

方法一：定义用户自定义的CPAN，通过CPAN安装DBI::mysql模块(orthomcl软件中mysqlInstallGuide.txt提供的安装方法)

Installing modules as a standard user

– Follow the steps below to install modules as a non-root user. We

assume /myperl in your home directory is your custom perl directory.

1. In your home directory, create the PERL and CPAN directories, and

a blank CPAN config module:

\$ mkdir myperl

\$ mkdir .cpan

\$ mkdir .cpan/CPAN

\$ echo “\$CPAN::Config = {}”> ~/.cpan/CPAN/MyConfig.pm

2. Configure your environment by adding the following to your

.bash_profile file in your home directory:

######################################

if [ -z “\$PERL5LIB” ]

then

# If PERL5LIB wasn’t previously defined, set it…

PERL5LIB=~/myperl/lib

else

# …otherwise, extend it.

PERL5LIB=$PER