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How to set up Blast2GO Local Database on Mac

Database is updated with GO database of 1/7/2017

Since Gene Ontology Consortium terminated to create GO Database dump file, we can't update Blast2GO database. When the new dump file becomes available, we will resume to update database. The date is not announced yet.

Here is the easiest and fastest procedure to set up Blast2Go local database on Mac. We provide pre-built database files. You will just download and unzip database files. Original instruction to create Blast2Go local database is found here. It takes more than 12 hours to create databases, if everything goes well.
Since Sep. 2016, GO database format has been changed and special handling is needed to create Blast2GO database.

With local database, Blast2Go mapping speed will be almost 250 times faster than that with the public database. Benchmark results are available here.
Even though you need to open Terminal and type some commands, you don't need to use mysql command. If you use OS X 10.8 Mountain Lion or earlier, some modifications may be needed.

The instruction for Windows is here, and for Linux is here.

Requirements

  • OS X 10.9.5 Mavericks, OS X 10.10.5 Yosemite, OS X 10.11.2 El Capitan. If you use different version of OS X, become our member and send request to us.
  • At least 200 GB disk space

How to set up

  • Log in to your Mac.
  • Make sure more than 200 GB space is available on your hard drive.
  • Click the database download links above and click Download Icon at the top of the page to download zip file. File names are mysql-201701.zip, b2gdb1-201701.zip, b2gdb2-201701.zip, b2gdb3-201701.zip, b2gdb4-201701.zip, b2gdb5-201701.zip, and b2gdb6-201701.zip. Total size is about 40 GB. go_monthly-assocdb-data.gz dated 1/7/2017 is used.
  • Double-click all downloaded zip files.
  • You will get mysql, b2gdb, b2gdb 2, b2gdb 3, b2gdb 4, b2gdb 5, and b2gdb 6 folders.
  • Move all files in b2gdb 2, b2gdb 3, b2gdb 4, b2gdb 5, and b2gdb 6 folders to b2gdb folder.
  • Number of files in b2gdb folder is 142.  Number of files in mysql folder is 69.  Unzipped total size is about 140 GB. We call the folder b2gdb and mysql folders reside as S folder.
  • Visit http://dev.mysql.com/downloads/mysql/5.6.html#downloads and download Mac OS X 10.9 (x86, 64-bit), DMG Archive.  Double-click downloaded dmg file to mount it.  Double-click mysql-5.6.27-osx10.8-x86_64.dmg (MySQL itself). Yes. Even though you download DMG for 10.9, pkg file is for 10.8. On OS X 10.11 El Capitan, you will get "Installer quit unexpectedly" dialog. Just Ignore it.
  • Go to System Preferences and open MySQL.
  • Stop MySQL server, if it is running.
  • Open Finder.
  • Go -> Go to Folder menu and enter /usr/local/mysql/data and click Go button.  You will see mysql folder, test folder, performance_schema folder and several files.  We call this folder as D folder.
  • Move mysql folder in D folder to Trash.
  • Copy mysql and b2gdb folders in S folder to D folder.
  • Open Applications/Utilities/Terminal.
  • Type "cd /usr/local/mysql/data" and type return.
  • In the Terminal Window, type "sudo chown -R _mysql:_mysql mysql" and type return.
  • In the Terminal Window, type "sudo chown -R _mysql:_mysql b2gdb" and type return.
  • Start MySQL server.  Confirm MySQL Server instance is running.
  • MySQL root password is b2groot. You can change it, if you want.
  • Launch Blast2Go version 2.8.
  • Go to Tools -> General Setting -> DataAccess Settings.
  • Select Own Database, type in parameters below and click OK.
              DB Name           b2gdb
              DB Host              localhost
              DB User              blast2go
              DB Password   blast4it
  • That’s it. Enjoy faster Blast2Go