• Software requirements
• Installation
• Optional software
• Supplied external software
• Replacing external software

Software Requirements

Required:

TCW v4.0.5 (July 2025): Test all TCW programs using the demo files, plus downloaded a UniProt database and GO with runAS and verified it worked. RunDE was tested with edgeR and goSeq.

TCW v4.0.4 (July 2022): Used to create multiple large TCW comparative projects with expression levels.

   tar -xvf TCW_4.tar.gz

   Executables:
       execLoadLib     execAssm        execAnno
       runAS           runDE           runSingleTCW    runMultiTCW
       viewSingleTCW   viewSingleTCW
   Directories:
       java/jars     Ext/mac    Ext/linux     doc
       R-scripts     scripts    projects
   Text files:
       HOSTS.cfg     README     LICENSE
	

   mysql -u <username> -p

Note:

• The user must have sufficient privileges to create a new database.
• If you will be using the optional assembly feature, Innodb table must be enabled.
• Execute "./runSingletTCW -v", which will check some variable that can influence execution times.
  Also see Trouble MySQL.

Step 3: Open the HOSTS.cfg file in an editor.

   DB_host=localhost
   DB_user=
   DB_password=
	

Step 4: Test external programs Check that the external programs have executable permissions. On linux, check Ext/linux; on MacOS x86_64, check Ext/mac; on MacOS M4 (aarch64), check Ext/macM4. You may want to run the compiled programs at the command line to see if they execute, e.g.

   ./diamond
   Error: Syntax: diamond COMMAND [OPTIONS]. To print help message: diamond help

Please read the section below on "Supplied external software.

Step 5: Run runAS (see Annotation Setup) to obtain UniProt files and GO database. Other annotation databases can also be used, but TCW provides GO support with UniProt.

RJava for DE (differential expression)

   >install.packages("rJava")
   >system.file("jri", package="rJava")

Step 2. Edit the runDE script, uncomment the correct path or change to the correct path:

   #JPATH=/usr/lib64/R/library/rJava/jri				# e.g. linux

   #JPATH=/Library/Frameworks/R.framework/Resources/library/rJava/jri	# e.g. Mac

Step 3. You must set the R_HOME environment variable, e.g.

   export R_HOME=/usr/lib64/R                              # for Linux using bash or zsh

   export R_HOME=/Library/Frameworks/R.framework/Resources # for MacOS using bash or zsh

R packages for DE

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

OrthoMCL is also supplied for runMultiTCW, but disabled. The /Ext/mac and /Ext/linux directories have the code with a README.TCW on how to make them work within TCW.

By default, /Ext/macM4 does not have CAP3 or Muscle. These programs will not be available from the interface unless the user provides them.

MacOS Verify Catalina and later versions require verification of external software. See (see Running Ext/mac external programs).

The references for all TCW external software are provided in external references

The only external source code supplied is MstatX and OrthoMCL because files had to be changed for it to work.

Blast and Diamond

1. You can define where the executables are in the HOSTS.cfg file using the blast_path and diamond_path parameters, e.g.

      blast_path = /Users/cari/Workspace/bin/blast
      diamond_path = /Users/cari/Workspace/bin/diamond
   

2. Use the default ones in /Ext.

3. If you have Blast and/or Diamond in a bin that is accessed by your PATH environmental variable, and want to use them, just remove the existing directory from /Ext/linux or /Ext/mac.

   blast_path = /Users/cari/Workspace/TCW_4/Ext/mac/blast

   ./runSingleTCW -v