From 5af2a4ebeb3fe63628d41b453da735f401391f1d Mon Sep 17 00:00:00 2001 From: Cao T Date: Wed, 10 Oct 2018 12:41:39 -0400 Subject: [PATCH 1/2] Update README.md --- README.md | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/README.md b/README.md index d3a8931..432a7e6 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: /share/apps/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).** From d9623e1e9d09f06f3c5830f94d6fdcf9a94af52e Mon Sep 17 00:00:00 2001 From: Cao T Date: Thu, 11 Oct 2018 10:16:06 -0400 Subject: [PATCH 2/2] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 432a7e6..ba437fe 100755 --- a/README.md +++ b/README.md @@ -54,7 +54,7 @@ diamond v0.8.15.77 | by Benjamin Buchfink Check http://github.com/bbuchfink/diamond for updates. #CPU threads: 12 -Database file: /share/apps/HLA.git/data/hla.faa +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]