From 813735d82b167b4e31838e35b07c4600d39f5617 Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Mon, 22 Mar 2021 16:41:00 +0100
Subject: [PATCH] species compose update
---
templates/gspecies_compose_template.yml.j2 | 15 +++++++++++----
1 file changed, 11 insertions(+), 4 deletions(-)
diff --git a/templates/gspecies_compose_template.yml.j2 b/templates/gspecies_compose_template.yml.j2
index bee4b25..ef300ae 100644
--- a/templates/gspecies_compose_template.yml.j2
+++ b/templates/gspecies_compose_template.yml.j2
@@ -136,7 +136,15 @@ services:
image: quay.io/galaxy-genome-annotation/docker-galaxy-annotation:gmod
volumes:
- ../galaxy_data_libs_SI.py:/opt/galaxy_data_libs_SI.py
- #- ./docker_data/galaxy/:/export/ # Commented for testing TODO: Uncomment in production
+ {% if persist_galaxy_data is defined %}
+ {% if persist_galaxy_data == "False" %}
+ #- ./docker_data/galaxy/:/export/
+ {% else %}
+ - ./docker_data/galaxy/:/export/
+ {% endif %}
+ {% else %}
+ - ./docker_data/galaxy/:/export/
+ {% endif %}
- ./src_data/:/project_data/:ro
#- /groups/XXX/:/groups/XXX/:ro # We do this when we have symlinks in src_data pointing to /groups/XXX/...
- ./docker_data/jbrowse/:/jbrowse/data/
@@ -148,12 +156,11 @@ services:
GALAXY_CONFIG_BRAND: "{{ Genus }} {{ species }}"
GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE: "True"
GALAXY_CONFIG_USE_REMOTE_USER: "True"
- GALAXY_CONFIG_REMOTE_USER_MAILDOMAIN: "sb-roscoff.fr"
+ GALAXY_CONFIG_REMOTE_USER_MAILDOMAIN: "{{ galaxy_config_remote_user_maildomain }}"
GALAXY_DEFAULT_ADMIN_EMAIL: "{{ galaxy_default_admin_email }}"
GALAXY_DEFAULT_ADMIN_USER: "{{ galaxy_defaut_admin_user }}"
GALAXY_DEFAULT_ADMIN_PASSWORD: "{{ galaxy_default_admin_password }}"
- GALAXY_CONFIG_ADMIN_USERS: "admin@galaxy.org, gga@sb-roscoff.fr" # admin@galaxy.org is the default (leave it), gogepp@bipaa is a shared ldap user we use to connect
- GALAXY_CONFIG_MASTER_API_KEY: "{{ galaxy_config_master_api_key }}"
+ GALAXY_CONFIG_ADMIN_USERS: "admin@galaxy.org, {{ galaxy_default_admin_email }}" # admin@galaxy.org is the default (leave it), gogepp@bipaa is a shared ldap user we use to connect
ENABLE_FIX_PERMS: 0
PROXY_PREFIX: /sp/{{ genus_species }}/galaxy
GALAXY_TRIPAL_URL: http://tripal.{{ genus_species }}/tripal/
--
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