----------------------------------- INSTRUCTIONS TO RUN LD CALCULATIONS ----------------------------------- In order to run LD calculations, either using the API or the webcode, you will need: 1 - Download and compile htslib. Note if you have already installed the ensembl-io module you may already have htslib: cd [your_local_sw_dir] git clone --branch master --depth 1 https://github.com/samtools/htslib.git cd htslib make cd - export HTSLIB_DIR=[your_local_sw_dir]/htslib 2 - Compile the C code present in this directory (ensembl-variation/C_code), called calc_genotypes.c and ld_vcf.c. You can compile the code doing: make if the gcc compiler is installed in your system. Otherwise, you will need to find out which C compiler you have installed and modify the CC variable in the Makefile pointing to your compiler (icc,...) You need to copy the created binary files (calc_genotypes and ld_vcf) to one of the directories in your path in order for the API code to find it or add this directory (ensembl-variation/C_code) in your path doing something like set path = ($path (your_path_to_ensembl_code)/ensembl-variation/C_code)