From e2e2812b1a0f9390bbabdb50c4f8cc8fccb7349c Mon Sep 17 00:00:00 2001
From: danknights <danknights@gmail.com>
Date: Thu, 1 Mar 2018 14:06:08 -0600
Subject: [PATCH] Update README.md

---
 README.md | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/README.md b/README.md
index 1e10a44..6f56820 100644
--- a/README.md
+++ b/README.md
@@ -246,3 +246,30 @@ Options:
                        /home/grad00/hillm096/results-171106]
   -h, --help           Show this message and exit.
 ```
+
+
+## Database creation.
+To create a BURST database for SHOGUN, follow instructions on the BURST github page to create an acx and edx file with the same base filename, then create a file called "metadata.yaml" in the same folder, with an entry `burst: <basename>`, as in this example:
+(https://github.com/knights-lab/SHOGUN/blob/master/shogun/tests/data/metadata.yaml)[https://github.com/knights-lab/SHOGUN/blob/master/shogun/tests/data/metadata.yaml]
+
+You will need a taxonomy file formatted as in the `genomes.small.tax` file (here)[https://github.com/knights-lab/SHOGUN/tree/master/shogun/tests/data] to provide taxonomy. Add an entry to the yaml file with a key `general:` and a sub-key `taxonomy: <taxonomy file name>`. A bowtie2 database base filename and Utree database filename may be added as follows:
+```
+general:
+  taxonomy: genomes.small.tax
+  fasta: genomes.small.fna
+  shear: sheared_bayes.fixed.txt
+function: function/ko
+burst: burst/genomes.small
+bowtie2: bowtie2/genomes.small
+utree: utree/genomes.small
+```
+
+A functional database is optional. Examples are shown (here)[https://github.com/knights-lab/SHOGUN/tree/master/shogun/tests/data/function].
+
+All database files for BURST, Bowtie2, and Utree should be in the same parent folder. Once the folder is created and the `metadata.yaml` file is populated as in the above example, the new database may be used in SHOGUN as follows:
+
+```
+shogun pipeline -i input.fna -d /path/to/database/parent/folder/ -o output -m burst
+shogun pipeline -i input.fna -d /path/to/database/parent/folder/ -o output -m utree
+shogun pipeline -i input.fna -d /path/to/database/parent/folder/ -o output -m bowtie2
+```