• Problems on Mac
• Installation on MacOS 10.15.4 (May2020)
• Running /Ext/mac external programs

Problems on Mac

• 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 hidden window.
• The buttons are all white.
• The UniProt search links do not work; hence, is not provided on Mac.

Installation on MacOS 10.5.4 (Catalina)

MySQL

1. Download from dev.mysql.com mysql-8.0.17-macos10.14-x86_64.dmg. Click the '.dmg' file and follow the instructions.

2. There will be a mySQL icon on your System Preferences, where you can start/stop the MySQL server.
    
3. 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;
   			

4. 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

1. Download from cran R the file R-4.0.0.pkg. Click to install.

2. Type 'R' at the terminal prompt, then the following:

   >install.packages("rJava")
   >if (!requireNamespace("biocManager", quietly=TRUE))
   >install.packages("BiocManager")
   >BiocManager::install(version = "3.11")
   >BiocManager::install("edgeR")
   >BiocManager::install("goseq")
   >BiocManager::install("DESeq2")
   

3. Set your $R_HOME:

   setenv R_HOME /Library/Frameworks/R.framework/Resources  # tcsh
   export R_HOME=/Library/Frameworks/R.framework/Resources  # zcsh
   

4. Make sure runDE has the following:

   -Djava.library.path=/Library/Frameworks/R.Framework/Resources/library/rJava/jri
   

Perl-mySQL interface

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]
 make
 make test
 sudo make install
 sudo ln -s /usr/local/mysql/lib/libmysqlclient.18.dylib /usr/lib/libmysqlclient.18.dylib

Running /Ext/mac external programs

1. Bring up the System Setting, select Privacy&Security.
2. Run TCW Annotate. It will popup a window with 'diamond Not Open'; select Done.
3. On the Privacy window, it will now show 'diamond was blocked to protect your Mac.'; select Allow Anyway.
4. Run TCW Annotate. It will popup 'Open diamond?'; select Open Anyway.
5. It will then popup a window asking for your password. Finally, diamond will run.

I had to do the same for makeblastdb, blast and tblastx for the runSingleTCW pair alignment. It was easiest to just keep running Annotate until they were all authenticated.

For runMultiTCW MSA computations, I had to authenticate all the following in the mafftdir directory:

  bin/
  mafft
  libexec/
    version
    countlen
    splittbfast
    tbfast
    disttbfast
    dvtditr
    f2cl

There may be an easier way to do this, but this works.

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