Running TCW on MacOS
The following includes:
Problems on Mac
I've run TCW extensively on my Mac, and found a few slight Java problems:
- In runSingleTCW and runMultiTCW, the interface does not always automatically update until I click in the window.
- Pop-up windows can get hidden behind the main window, and it makes TCW appear to be frozen -- move the main TCW window to find the
- The buttons are all white, and the highlighting on the GO tree is very light. Occasionally, the highlighting causes text to disappear.
- The UniProt search links do not work; hence, are not provided on Mac.
Installation on MacOS 10.5.4 (Catalina)
Here are my notes from my installation on my personal Mac v10.15 with Java v14.0.1 (May 2020). It is necessary
to use TCW v5.0.3 or higher with MySQL v8.
- Download from
Click the '.dmg' file and follow the instructions.
There will be a mySQL icon on your System Preferences, where you can start/stop the MySQL server.
- Test: I use tcsh, so I enter the following into the .tcshrc file:
alias mys '/usr/local/mysql/bin/mysql -u root -p[password]'
From the command line, I execute source .tcshrc. If you are using zch or bash, you will need to use their equivalent commands.
From the command line, enter 'mys', and then at the prompt:
>create database mytest;
>drop database mytest;
- In the HOSTS.cfg of the TCW package, set DB_user=[mysql userid], DB_password=[mysql password]
At this point, can build databases and view them.
However, you will not be able to run DE calculations without installing R, or OrthoMCL
without installing the Perl-mysql interface.
R and R-Java interface
- Download from the
file R-4.0.0.pkg. Click to install.
- Type 'R' at the terminal prompt, then the following:
>if (!requireNamespace("biocManager", quietly=TRUE))
>BiocManager::install(version = "3.11")
- Set your $R_HOME:
setenv R_HOME /Library/Frameworks/R.framework/Resources # tcsh
export R_HOME=/Library/Frameworks/R.framework/Resources # zcsh
- Make sure runDE has the following:
I could not get this working on Catalina.
The following instructions are from an earlier version of this document (for MacOS 10.9.5):
added 'set $path=($path /usr/local/perl/bin)' to my .tcshrc
>cpan install DBD::mysql
cd .cpan/build/DBD-mysql-4.029-[a unique string will end this directory name]
sudo ln -s /usr/local/mysql/lib/*.dylib
perl Makefile.PL --testuser=[mysql userid] --testpassword=[mysql password]
sudo make install
sudo ln -s /usr/local/mysql/lib/libmysqlclient.18.dylib /usr/lib/libmysqlclient.18.dylib
Running /Ext/mac external programs
MacOS 10.15 has made it difficult to run programs downloaded from the web unless its been
authenticated by Apple. Running external programs from TCW,
you will either get popup that states "xxx cannot be opened because developer cannot be verified", or
the program will just fail. Do the following:
I did not have to do this for Blast, but I did need to do it for the other /Ext/mac programs.
All were straight-forward except for mafft; I had to authenticate all the following in the mafftdir
- Using the Finder, select the program and Open With "Terminal" or "iTerm".
- You will get a pop-up, select "Open".
- After that, you will be able to run it via TCW.
There is a way to allow any downloaded program to execute by using:
sudo spctl --master-disable
Then in Preferences, Security&Privacy, General, select 'anywhere'. I did not try this.