安装Orthomcl

最新推荐文章于 2024-03-03 21:21:23 发布

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最新推荐文章于 2024-03-03 21:21:23 发布

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分类专栏：生物信息软件

本文链接：https://blog.csdn.net/java31/article/details/104959843

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1、 Install vmwareworkstationrj12.0.0.64202.1442972430

Sn:ZU5NU-2XWD2-0806Z-WMP5G-NUHV6
2、 Use ubuntu-16.04.5-desktop-amd64.iso
3、 change apt-get source by aliyun

sudo mv /etc/apt/sources.list /etc/apt/sources.list.bak
sudo vi /etc/apt/sources.list

deb-src http://archive.ubuntu.com/ubuntu xenial main restricted #Added by software-properties
deb http://mirrors.aliyun.com/ubuntu/ xenial main restricted
deb-src http://mirrors.aliyun.com/ubuntu/ xenial main restricted multiverse universe #Added by software-properties
deb http://mirrors.aliyun.com/ubuntu/ xenial-updates main restricted
deb-src http://mirrors.aliyun.com/ubuntu/ xenial-updates main restricted multiverse universe #Added by software-properties
deb http://mirrors.aliyun.com/ubuntu/ xenial universe
deb http://mirrors.aliyun.com/ubuntu/ xenial-updates universe
deb http://mirrors.aliyun.com/ubuntu/ xenial multiverse
deb http://mirrors.aliyun.com/ubuntu/ xenial-updates multiverse
deb http://mirrors.aliyun.com/ubuntu/ xenial-backports main restricted universe multiverse
deb-src http://mirrors.aliyun.com/ubuntu/ xenial-backports main restricted universe multiverse #Added by software-properties
deb http://archive.canonical.com/ubuntu xenial partner
deb-src http://archive.canonical.com/ubuntu xenial partner
deb http://mirrors.aliyun.com/ubuntu/ xenial-security main restricted
deb-src http://mirrors.aliyun.com/ubuntu/ xenial-security main restricted multiverse universe #Added by software-properties
deb http://mirrors.aliyun.com/ubuntu/ xenial-security universe
deb http://mirrors.aliyun.com/ubuntu/ xenial-security multiverse

sudo apt-get update

4、 ubuntu configure

sudo apt-get install openssh-server
sudo apt-get install git
sudo apt-get remove vim-tiny
sudo apt-get remove vim-common
sudo apt-get install vim

5、 apt-get setup mysql5.7

wget https://dev.mysql.com/get/mysql-apt-config_0.8.1-1_all.deb
sudo dpkg -i mysql-apt-config_0.8.1-1_all.deb,select 5.7,ok
wget http://repo.mysql.com/RPM-GPG-KEY-mysql
sudo apt-key add RPM-GPG-KEY-mysql
sudo apt-get update
sudo apt-get install mysql-server
input password
mysql –u root –p
GRANT ALL PRIVILEGES ON *.* TO 'root'@'%' IDENTIFIED BY 'password' WITH GRANT OPTION;
FLUSH PRIVILEGES;quit
sudo service mysql restart

6、 perl package

sudo apt-get install cpanminus
sudo cpanm --mirror http://mirrors.163.com/cpan --mirror-only CGI::Session
cpanm BioPerl DBD::mysql DBI Parallel::ForkManager YAML::Tiny Set::Scalar Text::Table Exception::Class Test::Most Test::Warn Test::Exception Test::Deep Moose SVG Algorithm::Combinatorics
cpanm Algorithm::Combinatorics

7、 orthomcl

git clone https://github.com/apetkau/orthomcl-pipeline.git
sudo apt-get install mcl
wget http://orthomcl.org/common/downloads/software/v2.0/orthomclSoftware-v2.0.9.tar.gz
#download BLAST2 v2.2.26
vi ~/.bashrc
export PATH=$PATH:/path/to/blast-2.2.26/bin
export PATH=$PATH:/path/to/orthomcl/bin

mysql –u root –p
create user 'orthomcl' identified by 'java31password';
GRANT ALL PRIVILEGES on *.* to 'orthomcl' WITH GRANT OPTION;
FLUSH PRIVILEGES;quit
pwd /home/san/work/orthomcl-pipeline
perl scripts/orthomcl-setup-database.pl --user orthomcl --password java31password --host localhost --database orthomcl --outfile orthomcl.con
perl t/test_pipeline.pl -m orthomcl.conf -s fork -t /tmp

8、 library