INSTALL

** Installation of Cortex itself

1. Run the install bash script

 bash install.sh


2. To compile Cortex for 1 colour and kmers between 1 and 31:

make cortex_var

  generates a binary/executable in bin/ called cortex_var_31_c1

  To compile Cortex for 172 colours and kmers between 33 and 63, type

make NUM_COLS=172 MAXK=63 cortex_var


If this fails, consult the manual at : http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf




** Other packages/set-up required for run_calls.pl and for dumping VCFs

1. Git clone minimap2 from https://github.com/lh3/minimap2
   Cd into it and type make. This produces the minimap2 executable.
   The run_calls.pl and process_calls.pl will need to know where this executable is (I pass the path in as an argument)


2. Obtain VCFTools from
   http://sourceforge.net/projects/vcftools/files/vcftools_0.1.9.tar.gz
   or an equivalent. It is not enough to know it is installed somewhere on your system by someone,
   process_calls and run_calls will need to be given the path to the vcftools_0.1.9/ directory (or whichever
   version you get)

3. Add 
   /path/to/CORTEX_release_v_whatever/scripts/analyse_variants/bioinf-perl/lib/
   and
   /path/to/CORTEX_release_v_whatever/scripts/calling/
   to your PERL5LIB

4. Add /path/to/CORTEX_release_v_whatever/scripts/analyse_variants/needleman_wunsch/ to your PATH