From 6f91521c13fdf073a1d27c9f71eb076aa4a26300 Mon Sep 17 00:00:00 2001
From: Thomas Sibley <tsibley@fredhutch.org>
Date: Thu, 14 Sep 2023 13:43:02 -0700
Subject: [PATCH] Configure Nextstrain CLI to use the ambient runtime inside
 this runtime
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If users enter a `nextstrain shell` with this Docker runtime, we want
`nextstrain` inside that to use the ambient environment.

Reported by @corneliusroemer in Slack.¹

¹ <https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1694718932379359>
---
 Dockerfile | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index 6d61742..fd11c23 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -493,6 +493,13 @@ RUN useradd nextstrain \
     --home-dir /nextstrain \
     --no-log-init
 
+# No nesting of runtimes, please.  Use the ambient runtime inside this runtime.
+ENV NEXTSTRAIN_HOME=/nextstrain
+RUN nextstrain check-setup --set-default ambient \
+ && chown nextstrain:nextstrain /nextstrain/config \
+ && chmod a+rw /nextstrain/config \
+ && rm -f /nextstrain/lock
+
 # The host should bind mount the pathogen build dir into /nextstrain/build.
 WORKDIR /nextstrain/build
 RUN chown nextstrain:nextstrain /nextstrain/build