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caot Oct 10, 2018
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20 changes: 20 additions & 0 deletions README.md
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Expand Up @@ -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 <buchfink@gmail.com>
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).**

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