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Migrate subdomain microgalaxy and microbiome to microbiology #1415

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Feb 24, 2025
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Migrate subdomain microgalaxy and microbiome to microbiology #1415

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26 changes: 26 additions & 0 deletions files/galaxy/subdomains/microbiology/static/welcome.html
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Original file line number Diff line number Diff line change
@@ -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>
1 change: 1 addition & 0 deletions files/traefik/rules/template-subdomains.yml
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Expand Up @@ -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"}}
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1 change: 1 addition & 0 deletions group_vars/gxconfig.yml
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions group_vars/sn06/subdomains.yml
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Expand Up @@ -96,6 +96,7 @@ galaxy_themes_subdomains:
- name: metagenomics
- name: microbiome
- name: microgalaxy
- name: microbiology
- name: rna
- name: graphclust
- name: ecology
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18 changes: 11 additions & 7 deletions templates/galaxy/config/global_host_filters.py.j2
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Expand Up @@ -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" ]
Expand Down Expand Up @@ -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': [
Expand Down Expand Up @@ -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",
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20 changes: 10 additions & 10 deletions templates/nginx/galaxy-main.j2
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Expand Up @@ -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 {
Expand All @@ -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;
}
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