Merge pull request #1415 from sanjaysrikakulam/microbiology_subdomain

Migrate subdomain microgalaxy and microbiome to microbiology
usegalaxy-eu · Feb 24, 2025 · 11c9061 · 11c9061
2 parents de9a0e3 + 7dbd5cf
commit 11c9061
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Showing 6 changed files with 50 additions and 17 deletions.
diff --git a/files/galaxy/subdomains/microbiology/static/welcome.html b/files/galaxy/subdomains/microbiology/static/welcome.html
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+<style>
+body, html { width:100% ;
+    height:100% ;
+    overflow:hidden ;
+}
+iframe { width:100% ;
+        height:100% ;
+    border:none ;
+    position: absolute;
+    top: -9999em;
+    visibility: hidden;
+}
+</style>
+</head>
+<body style="margin:0px">
+    <iframe id='center-iframe' src="" height="100%" onload="this.style.position='static'; this.style.visibility='visible';"></iframe>
+<script type="text/javascript">
+var pseudo_rand = parseInt(Date.now() / 1000 / 60 / 10);
+document.getElementById('center-iframe').src = 'https://labs.usegalaxy.org.au/?content_root=https://github.com/galaxyproject/galaxy_codex/blob/main/communities/microgalaxy/lab/usegalaxy.eu.yml';
+</script>
+</body>
+</html>
diff --git a/files/traefik/rules/template-subdomains.yml b/files/traefik/rules/template-subdomains.yml
@@ -25,6 +25,7 @@ http:
 {{template "subdomain" "metagenomics"}}
 {{template "subdomain" "microbiome"}}
 {{template "subdomain" "microgalaxy"}}
+{{template "subdomain" "microbiology"}}
 {{template "subdomain" "rna"}}
 {{template "subdomain" "graphclust"}}
 {{template "subdomain" "ecology"}}

diff --git a/group_vars/gxconfig.yml b/group_vars/gxconfig.yml
@@ -1062,6 +1062,7 @@ base_app_main: &BASE_APP_MAIN
     'metagenomics.usegalaxy.eu': Metagenomics
     'microbiome.usegalaxy.eu': Microbiome
     'microgalaxy.usegalaxy.eu': microGalaxy
+    'microbiology.usegalaxy.eu': Microbiology
     'rna.usegalaxy.eu': RNA
     'graphclust.usegalaxy.eu': GraphClust
     'ecology.usegalaxy.eu': Ecology

diff --git a/group_vars/sn06/subdomains.yml b/group_vars/sn06/subdomains.yml
@@ -96,6 +96,7 @@ galaxy_themes_subdomains:
   - name: metagenomics
   - name: microbiome
   - name: microgalaxy
+  - name: microbiology
   - name: rna
   - name: graphclust
   - name: ecology

diff --git a/templates/galaxy/config/global_host_filters.py.j2 b/templates/galaxy/config/global_host_filters.py.j2
@@ -22,11 +22,11 @@ def per_host_tool_labels( context, label ):
     # hide genomics label in the single cell subdomain
     if label.id == "genomics_label" and subdomain == "singlecell":
         return False
-        
+
     # show earth-system labels only in that subdomain
     if label.id.startswith("earth-system-label"):
         return subdomain == "earth-system"
-        
+
     # Core tools used by all virtual hosts.
     valid_labels = [ "file_meta_label", "general_text_label"]
     general_ngs_labels = [ "genomics_label" ]
@@ -113,6 +113,10 @@ DOMAIN_SECTIONS = {
         "multiple_alignments", "assembly", "annotation",
         "graph_display_data", "metagenomic_analysis", "mothur", "qiime",
         "biom_manipulation", "interactivetools", "nanopore", "ncbi_blast", 'metabolomics'],
+    'microbiology': GENERAL_NGS_SECTIONS + ["fasta_fastq_manipulation",
+        "multiple_alignments", "assembly", "annotation",
+        "graph_display_data", "metagenomic_analysis", "mothur", "qiime",
+        "biom_manipulation", "interactivetools", "nanopore", "ncbi_blast", 'metabolomics'],
     'rna': GENERAL_NGS_SECTIONS + ["rna_seq", "annotation", "rna_analysis",
         "graph_display_data"],
     'singlecell': [
@@ -159,11 +163,11 @@ DOMAIN_SECTIONS = {
     'materials': ['muon_spectroscopy', 'xas'],
     'aqua': ["climate_analysis", "gis_data_handling", "graph_display_data", "interactivetools", "machine_learning"],
     'earth-system': [
-        "earth-system-section-watercoastal", 
-        "earth-system-section-earthcritical", 
-        "earth-system-section-volcano", 
-        "earth-system-section-biogeo", 
-        "earth-system-section-marineomics", 
+        "earth-system-section-watercoastal",
+        "earth-system-section-earthcritical",
+        "earth-system-section-volcano",
+        "earth-system-section-biogeo",
+        "earth-system-section-marineomics",
         "earth-system-section-interactivetools",
         "biodiversity_data_exploration",
         "annotation",

diff --git a/templates/nginx/galaxy-main.j2 b/templates/nginx/galaxy-main.j2
@@ -287,16 +287,6 @@ server {
 	add_header X-Robots-Tag none;
 
 	client_max_body_size 1G; # aka max upload size, defaults to 1M
-
-	# BY-COVID federated analysis demonstration data (restricted access demo)
-	location /federated_analysis_data {
-		alias /data/dnb01/federated_analysis_demo_data/;
-		allow 10.5.68.0/24;
-		# BE instance IPs
-		allow 10.113.3.8;
-		allow 10.113.3.13;
-		deny all;
-	}
 }
 
 server {
@@ -307,3 +297,13 @@ server {
 
     return 302 $scheme://singlecell.usegalaxy.eu$request_uri;
 }
+
+
+server {
+    listen 443 ssl;
+    listen [::]:443 ssl;
+
+    server_name microgalaxy.usegalaxy.eu microbiome.usegalaxy.eu;
+
+    return 302 $scheme://microbiology.usegalaxy.eu$request_uri;
+}