diff --git a/README.md b/README.md index d3a8931..ba437fe 100755 --- a/README.md +++ b/README.md @@ -46,6 +46,26 @@ docker run -v `pwd`:`pwd` -w `pwd` humanlongevity/hla \ --output_path test ``` +Here is how to run it in none-docker environment +------------------------------------------------ +``` +$ diamond makedb --in /PATH-TO/HLA.git/data/hla.faa --db /PATH-TO/HLA.git/data/hla.dmnd +diamond v0.8.15.77 | by Benjamin Buchfink +Check http://github.com/bbuchfink/diamond for updates. + +#CPU threads: 12 +Database file: /PATH-TO/HLA.git/data/hla.faa +Opening the database file... [0.046007s] +Loading sequence data (0 sequences processed)... [0.170403s] +Writing trailer... [0.001012s] +Closing the database file... [0.034115s] +Processed 27618 sequences, 2118355 letters. +Total time = 0.251665s + +# Here is how to run a sample +$ run.py --sample_id test --input_bam_path tests/test.bam --output_path test +``` + For other types of BAMs, pre-processing is required. **Please check details [here](https://github.com/humanlongevity/HLA/wiki/BAMs-compatible-with-xHLA).**