From 6d44b97dafab0cca7cab324be95f6a99bef4026c Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Mon, 22 Mar 2021 15:28:29 +0100
Subject: [PATCH] elasticsearch memory lock removed
---
templates/gspecies_compose_template.yml.j2 | 16 +++++++++++++++-
1 file changed, 15 insertions(+), 1 deletion(-)
diff --git a/templates/gspecies_compose_template.yml.j2 b/templates/gspecies_compose_template.yml.j2
index 0ef71b1..9963b5e 100644
--- a/templates/gspecies_compose_template.yml.j2
+++ b/templates/gspecies_compose_template.yml.j2
@@ -56,10 +56,22 @@ services:
ENABLE_JBROWSE: /jbrowse/?data=data/{{ genus_species_sex }}
# This ENABLE_JBROWSE variable should point to the "best assembly" by default --> tag it in the input file and use it to define this variable correctly (also called
# unique id in the jbrowse tool parameters == both have to be identical)
+ {% if apollo == "True %}
+ ENABLE_APOLLO: 1
+ {% else %}
ENABLE_APOLLO: 0
+ {% endif %}
+ {% if blast == "True" %}
ENABLE_BLAST: 1
+ {% else %}
+ ENABLE_BLAST: 0
+ {% endif %}
ENABLE_DOWNLOAD: 1
+ {% if wiki == "True" %}
+ ENABLE_WIKI: 1
+ {% else %}
ENABLE_WIKI: 0
+ {% endif %}
ENABLE_GO: 0
ENABLE_ORTHOLOGY: 0
ENABLE_ORTHOLOGY_LINKS: 0
@@ -108,7 +120,7 @@ services:
volumes:
- ./docker_data/elastic_search_index/:/usr/share/elasticsearch/data/
environment:
- bootstrap.memory_lock: "true"
+ # bootstrap.memory_lock: "true"
xpack.security.enabled: "false"
xpack.monitoring.enabled: "false"
xpack.ml.enabled: "false"
@@ -209,6 +221,7 @@ services:
max_attempts: 3
window: 120s
+ {% if blast == "True" %}
blast:
image: quay.io/abretaud/sf-blast:latest
depends_on:
@@ -278,6 +291,7 @@ services:
- ./docker_data/blast_db/:/var/lib/postgresql/data/
networks:
- {{ genus_species }}
+ {% endif %}
# wiki:
# image: quay.io/abretaud/mediawiki
--
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