From 33da6be4710e77ce69f4b594f14c1674cf7c6ff0 Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Fri, 3 May 2024 08:23:17 -0400
Subject: [PATCH] docs: update readme (install seqrepo, uta/seqrepo test cmd, +
 submodules) (#406)

---
 README.md | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 8f44a298..dc19546b 100644
--- a/README.md
+++ b/README.md
@@ -82,9 +82,10 @@ First, you must install a local [SeqRepo](https://github.com/biocommons/biocommo
 ```shell
 pip install seqrepo
 export SEQREPO_VERSION=2021-01-29  # or newer if available -- check `seqrepo list-remote-instances`
-sudo mkdir /usr/local/share/seqrepo
+sudo mkdir -p /usr/local/share/seqrepo
 sudo chown $USER /usr/local/share/seqrepo
 seqrepo pull -i $SEQREPO_VERSION
+seqrepo update-latest
 ```
 
 If you encounter a permission error similar to the one below:
@@ -138,8 +139,8 @@ nearly instantaneous.
 You can test UTA and seqrepo installations like so:
 
 ```shell
-$ psql -XAt postgres://anonymous@localhost/uta -c 'select count(*) from transcript'
-249909
+$ psql -XAt postgres://anonymous@localhost/uta -c 'select count(*) from uta_20210129b.transcript'
+314227
 ```
 
 ##### It doesn't work
@@ -200,6 +201,12 @@ make devready
 source venv/3.10/bin/activate
 ```
 
+If you already cloned the repo, but forgot to include `--recurse-submodules` you can run:
+
+```shell
+git submodule update --init --recursive
+```
+
 #### Submodules
 
 vrs-python embeds vrs as a submodule, only for testing purposes. When checking out vrs-python and switching