Merge branch 'master' of gitlab.svi.edu.au:biocellgen-public/sscocaller

README.md

 ## sscocaller: Calling crossovers from single-sperm DNA sequencing reads
 
 It takes the large bam file which contains aligned DNA reads from a list of single sperm cells and summarizes allele
-counts for informative SNP markers. A HMM model is applied for haplotypin each sperm and viterbi algorithm is run
+counts for informative SNP markers. A HMM model is applied for haplotyping each sperm and viterbi algorithm is run
 for deriving the inferred haplotype sequence against the list of SNP markers.
 
 ## Inputs
@@ -39,3 +39,31 @@ Options:
 Examples
     ./sscocaller --threads 10 AAAGTAGCACGTCTCT-1.raw.bam AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz barcodeFile.tsv ./percell/ccsnp-
 ```
+
+
+## Setup/installation
+
+`sscocaller` uses `hts-nim`(https://github.com/brentp/hts-nim) that requires the `hts-lib` library. If you are building the `sscocaller` from
+source, you would need to install `hts-lib`
+
+```
+git clone --recursive https://github.com/samtools/htslib.git
+cd htslib && git checkout 1.10 && autoheader && autoconf && ./configure --enable-libcurl
+
+cd ..
+make -j 4 -C htslib
+export LD_LIBRARY_PATH=$HOME/htslib
+ls -lh $HOME/htslib/*.so
+```
+
+Then, `sscocaller` can be installed using `nimble`
+
+### Install with nimble
+
+`nimble install https://gitlab.svi.edu.au/biocellgen-public/sscocaller.git`
+
+The built binary in $HOME/.nimble/bin/sscocaller
+
+### Static builds
+
+The static bianry can be simply downloaded which works for GNU/Linux type OS:
\ No newline at end of file