From 9530b72544460ac396b7cdbbcdf19cf27e2f9d83 Mon Sep 17 00:00:00 2001
From: Kim Rutherford <kmr@aska.gen.nz>
Date: Tue, 28 Jan 2025 21:14:55 +1300
Subject: [PATCH] Create JBrowse instance, add assembly

Refs pombase/website#2038
---
 etc/docker-conf/Dockerfile-main | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/etc/docker-conf/Dockerfile-main b/etc/docker-conf/Dockerfile-main
index 536803f..9f4d121 100644
--- a/etc/docker-conf/Dockerfile-main
+++ b/etc/docker-conf/Dockerfile-main
@@ -117,6 +117,10 @@ COPY --chown=pombase:pombase conf/docker-healthcheck docker-healthcheck
 
 RUN (cd /var/www/html/jbrowse; ./bin/generate-names.pl)
 
+RUN (cd /pombase; jbrowse create jbrowse2; \
+     jbrowse add-assembly /pombase/bgzip_chromosomes/Schizosaccharomyces_pombe_all_chromosomes.fa.gz --name pombe_v1 --load copy --type bgzipFasta --out jbrowse2
+)
+
 RUN (cd pombase-website; ln -fs /pombase/main_config.json .; \
      cp etc/update_vars.sh /pombase/ && \
      npm install -g yarn; \