diff --git a/README.md b/README.md index 37df5837d90c5127c50834c832616d9b82e556c8..8eef208890e0ae6f589775cc3fab66a9f92fd2e2 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ ## 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