This page was last updated on Wednesday, 02-Jun-2021 10:33:43 CDT

Installation notes for OrthoMCL version 2.0.9 [18-jul-2013]

Old install notes for version 1.2

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Prerequisites

• mysql
• Blast
• MCL (Markov Clustering algorithm) see MCL Install Notes
• Perl modules
  1. This will be required to be able to install DBD::mysql
     $ sudo apt-get install libmysqlclient-dev
  2. $ sudo cpan Data::Dumper DBI DBD::mysql Bio::SearchIO Storable
  3. If install of DBD::mysql fails, it may need root password for mysql. Go to, for example
     /home/xxx/.cpan/build/DBD-mysql-4.029-PTdnLE
     and type sudo perl Makefile.PL --testuser=root --testpassword=rootpassword
  4. Check module installation. These two commands will produce no output if modules are installed
     $ perl -MDBI -e 1
  5. $ perl -MDBD::mysql -e 1

Installation

1. $ ver="2.0.9"
2. $ cd /programinstallers/
3. $ wget -N http://orthomcl.org/common/downloads/software/v2.0/orthomclSoftware-v$ver.tar.gz
4. $ cd /usr/local/bin/
5. $ tar -zxvf /programinstallers/orthomclSoftware-v$ver.tar.gz
6. Make a version-independent symlink
   $ ln -s orthomclSoftware-v$ver orthomclSoftware
7. Copy documentation to local web page
   $ cp -puv orthomclSoftware/doc/OrthoMCLEngine/Main/* /programinstallers/web/orthomcl/
8. Add to default PATH for all users
   $ sudo nano /etc/profile
   …
   PATH="$PATH:/usr/local/bin/orthomclSoftware/bin"
   …
9. Create a mysql database and a user
   $ mysql -h localhost -u root -p
10. Commands to show current users and databases
    > SELECT user, host, password, select_priv, insert_priv, shutdown_priv, grant_priv FROM mysql.user;
11. > SHOW databases;
12. Commands to create items required by OrthoMCL
    > CREATE USER 'orthomcl'@'localhost' IDENTIFIED BY 'password';
13. > CREATE database orthomcl;
14. > GRANT SELECT,INSERT,UPDATE,DELETE,CREATE VIEW,CREATE,INDEX,DROP ON orthomcl.* TO 'orthomcl'@'localhost';
15. > quit
16. $ cd /usr/local/bin/orthomclSoftware
17. Copy the configuration file templates to the root OrthoMCL directory so we can then edit them
    $ cp -puv doc/OrthoMCLEngine/Main/orthomcl.config.template orthomcl.config
18. $ cp -puv doc/OrthoMCLEngine/Main/mysql.cnf .
    In my case I had the existing file /etc/my.cnf and ~/.my.cnf as the mysql config files
19. $ nano orthomcl.config
    Change port back to default mysql port 3306,Remove port :3307, and if necessary append non-standard socket location:
    dbConnectString=dbi:mysql:orthomcl;mysql_socket=/nonstandardlocation/mysql/mysql.sock
    Fill in:
    dbLogin=orthomcl
    dbPassword=password
20. This is step 4 of the UserGuide.txt, but there is a typo there, this is correct
    $ orthomclInstallSchema orthomcl.config install_schema.log
21. Link to download protein sequences and ortholog groups
    https://orthomcl.org/orthomcl/app/downloads/
22. $