Current_install_instructions.txt

Varia comes with a script used to help install Varia, run Install_Varia.sh from the Varia directory and it will check whether the tools necessary for Varia 
are present in the users PATH. If it finds them, the path to them is reported. If it cannot find mcl or Circos, it will ask the user if they wish to 
install them using conda. For more commonly used tools such as Megablast or Samtools, it will not attempt to install them but will report them as missing 
from the PATH. The script also asks the user to select a database file and domains annotation to be used by Varia. The files are soft linked to and the 
links are stored in the vardb folder and domains folder respectively. This is to allow for a consistent file name to be used by Varia without modifying the 
existing file. To change the database or domains file, remove the links and rerun the installation script. Finally, the script reports the path to the 
Varia folder to be added to the user's PATH. 

1. Download Varia
2. unzip in directory you want to install Varia in
3. enter Varia1_5 directory
4. run Install_Varia.sh, this will:
	check if Varia can find samtools either stating the path to the version it will use or telling the user to install samtools
	check if Varia can find mcl, if it cant it will ask if the user wants to automatically install it with conda. If it can find mcl, then it will print the path to the version it will use
	check if Varia can find circos, if it cant it will ask if the user wants to automatically install it with conda. If it can find circos, then it will print the path to the version it will use
	check if Varia can find megablast, either stating the path to the version it will use or tell the user to intall megablast
	check if Varia can find formatdb, either stating the path to the version it will use or tell the user to intall formatdb
	check that there is a database registered in the correct format for megablast and will ask user which file to use if there isn't one.
	check that there is a domain file registered and will ask the user to select one if there isn't
	report the PATH to Varia1_5 that the user should add to their PATH
	Generate a log file summarising the installation

notes: 
-Varia.sh currently uses megablast, so ensuring megablast and formatdb are installed is essential. 
-The database and domains annotation included with Varia is an example database. The Pf3k database could not be included with Varia in part due to publication status and in part due to size of the database. It is recommended to download the Pf3K database of var genes and its accompanying domains annotation file for use with Varia.

-Varia creates soft links to databases and domain files. This is so the names of the files are correct for the Varia scripts to use, whilst ensuring the original files are not changed and don't need to be copied.

-To set the database for vardb, type yes when prompted then enter the exact path to the fasta file containing the database you wish to use. eg. /home/users/databases/Pf3k_var_genes.fasta.
-setting the domains file for Varia is handled the same as with setting the database and will require the path to their directory to be entered before their filename. eg. /home/user/domains/alternative_domains.fasta.

-there is a known issue with Circos and certain versions of perl. Circos will work on version 5.22.0 and earlier. Some more recent versions may not install Circos corectly due to a perl module not being updated correctly. Varia can run without Circos but will not be able to make Circos plots. So it is recommended to use perl 5.22.0 if possible.

5. Add the Varia1_5 directory to your PATH