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

Software Requirements

Required:

It has been tested on:

   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, check Ext/mac. 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

   >install.packages("rJava")

   #JPATH=/usr/lib64/R/library/rJava/jri
   #JPATH=Ext/linux/jri
   #echo Using Linux path

   #JPATH=Ext/mac/jri
   #JPATH=/Library/Frameworks/R.framework/Resources/library/rJava/jri
   #echo Using MAC-OS path

Step 3. You must set the R_HOME environment variable (confirm the path on your machine):

   setenv R_HOME /usr/lib64/R                              # for Linux using tcsh
   setenv R_HOME /Library/Frameworks/R.framework/Resources # for MacOS using tcsh

R packages for DE

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

• It did not work with MariaDB v10.4.12. It was fixed by editing the orthoLoadBlast script to set the MySQL local_infile from within the script. Also, orthoBlastParser was edited to accept ".fa" suffixes
• It works on MacOS 10.9, but has not been tested on MacOS 10.15 (problems with installing DBI:MySQL).
• If OrthoMCL does not work on your machine and you want an alternative to the TCW supplied clustering algorithms, you may download and run a ortholog computing program and then import the clusters using the runMultiTCW "User Supplied" option.

² MUSCLE and KaKs_Calculator in the /Ext/mac directory work for MacOS 10.15, but not for MacOS 10.9. For 10.9, move the MUSCLE and KaKS_Calculator from /Ext/mac0 to /Ext/mac, as these work. If your using MacOS 10.10 to 10.14, try them from the command line to see what works.

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