forked from bihealth/sodar-docker-compose
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathenv.example
206 lines (181 loc) · 6.45 KB
/
env.example
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
# This example environment is intended to be used with the "run.sh" script. If
# sets up SODAR with iRODS, Davrods, HTTPS using a provided certificate and
# iRODS PAM authentication via SODAR.
#
# Steps required to run this configuration:
#
# 1) Run ./init.sh
# 2) Add "127.0.0.1 sodar.local" into your /etc/hosts file.
# 3) Place your certificate .crt and .key files in config/traefik/tls.
# 4) Place a generated dhparams.pem file into config/irods/etc.
# 5) Bring up the docker compose network with ./run.sh.
# 6) Create superuser (see documentation)
# 7) Browse to https://sodar.local and sign in with the superuser account
# Docker network settings
NETWORK_BRIDGE_NAME=br-sodar
# Image versions
# NOTE: For the latest SODAR development build, use "dev-0"
# NOTE: If using the SOPDAR dev build, use the latest dev branch commit of this repository!
SODAR_SERVER_VERSION=0.14.2-0
IRODS_VERSION=4.2.11-1
SSSD_VERSION=1.16.5-10
# Logging
SODAR_LOGGING_LEVEL=ERROR
# Enabled SODAR backend plugins
SODAR_ENABLED_BACKEND_PLUGINS=appalerts_backend,omics_irods,ontologyaccess_backend,sodar_cache,taskflow,timeline_backend
# Secret key used for HTTP sessions, CHANGE FOR PRODUCTION
SODAR_DJANGO_SECRET_KEY=CHANGEMEchangemeCHANGEMEchangemeCHANGEMEchangemeCH
# Default admin user for SODAR, user must exist
SODAR_PROJECTROLES_DEFAULT_ADMIN=admin
# Allow local (non-LDAP) users
SODAR_PROJECTROLES_ALLOW_LOCAL_USERS=1
# Allow anonymous users to view the site
# NOTE: Also allows anonymous access to projects with public guest access
SODAR_PROJECTROLES_ALLOW_ANONYMOUS=0
# Default base URL for SODAR API, CHANGE FOR PRODUCTION
SODAR_API_DEFAULT_HOST=https://sodar.local
# Admin users for error email sending etc. (optional)
# Provide in the format "name:email,name:email"
SODAR_ADMINS=
# UI related settings
SODAR_SITE_INSTANCE_TITLE=ACME SODAR
SODAR_SITE_SUBTITLE=Docker
#
# Email sending (optional)
#
SODAR_PROJECTROLES_SEND_EMAIL=0
SODAR_EMAIL_SENDER=sodar@example.com
SODAR_EMAIL_SUBJECT_PREFIX=[ACME SODAR]
SODAR_EMAIL_URL=smtp://mail.example.com
# Custom email header and footer
SODAR_PROJECTROLES_EMAIL_HEADER=
SODAR_PROJECTROLES_EMAIL_FOOTER=
#
# Primary LDAP connection (optional)
#
SODAR_ENABLE_LDAP=0
SODAR_LDAP_DEBUG=0
SODAR_AUTH_LDAP_SERVER_URI=
SODAR_AUTH_LDAP_BIND_PASSWORD=
SODAR_AUTH_LDAP_BIND_DN=
SODAR_AUTH_LDAP_USER_SEARCH_BASE=
# USERNAME_DOMAIN is required to distinguish the LDAP accounts from
# local ones (e.g. 'user@DOMAIN') Must be all upper-case.
SODAR_AUTH_LDAP_USERNAME_DOMAIN=
SODAR_AUTH_LDAP_DOMAIN_PRINTABLE=
SODAR_AUTH_LDAP_START_TLS=
#
# CA_CERT_FILE is required if TLS is used and your LDAP server's CA
# is not a public one. It may be also used to restrict the check on your
# LDAP server's certificate for security reasons to a specific CA.
#
# To use it:
# - Put the right CA certificate into ./config/ldap/ldap_ca_cert.pem
# - Set SODAR_AUTH_LDAP_CA_CERT_FILE to /etc/ssl/certs/ldap_ca_cert.pem
#
SODAR_AUTH_LDAP_CA_CERT_FILE=
#
# USER_FILTER defaults to '(sAMAccountName=%(user)s)'.
# That is fine for ActiveDirectory users.
# People with POSIX account setup may need '(uid=%(user)s)' instead.
#
SODAR_AUTH_LDAP_USER_FILTER=
#
# Secondary LDAP connection (optional; primary required to work)
#
SODAR_ENABLE_LDAP_SECONDARY=0
SODAR_AUTH_LDAP2_SERVER_URI=
SODAR_AUTH_LDAP2_BIND_PASSWORD=
SODAR_AUTH_LDAP2_BIND_DN=
SODAR_AUTH_LDAP2_USER_SEARCH_BASE=
SODAR_AUTH_LDAP2_USERNAME_DOMAIN=
SODAR_AUTH_LDAP2_DOMAIN_PRINTABLE=
SODAR_AUTH_LDAP2_START_TLS=
SODAR_AUTH_LDAP2_CA_CERT_FILE=
SODAR_AUTH_LDAP2_USER_FILTER=
# Additional LDAP settings
SODAR_LDAP_ALT_DOMAINS=
#
# iRODS configuration
#
SODAR_ENABLE_IRODS=1
IRODS_HOST=irods
# Fully qualified domain name for iRODS server, if applicable
IRODS_HOST_FQDN=sodar.local
IRODS_PORT=1247
IRODS_ZONE=sodarZone
# Service user credentials to use, will be set on first run
IRODS_USER=rods
# Service user password, CHANGE FOR PRODUCTION
IRODS_PASS=rods
# Path to iRODS server certificate for iRODS client config (optional)
IRODS_CERT_PATH=/etc/traefik/tls/server.crt
# iRODS authentication scheme
IRODS_AUTHENTICATION_SCHEME=PAM
# iRODS client SSL verification (set to none if self-signed cert)
IRODS_SSL_VERIFY_SERVER=none
# Secret keys used by iRODS, CHANGE FOR PRODUCTION
IRODS_ZONE_KEY=TEMPORARY_zone_key
IRODS_NEGOTIATION_KEY=TEMPORARY_32byte_negotiation_key
IRODS_CONTROL_PLANE_KEY=TEMPORARY__32byte_ctrl_plane_key
IRODS_PASSWORD_SALT=tempsalt
# iRODS server SSL settings
IRODS_CLIENT_SERVER_NEGOTIATION=request_server_negotiation
IRODS_CLIENT_SERVER_POLICY=CS_NEG_REFUSE
IRODS_SSL_CERTIFICATE_CHAIN_FILE=/etc/traefik/tls/server.crt
IRODS_SSL_CERTIFICATE_KEY_FILE=/etc/traefik/tls/server.key
IRODS_SSL_DH_PARAMS_FILE=/etc/irods/dhparams.pem
# Path for SODAR collections within zone (leave empty if in zone root)
IRODS_ROOT_PATH=
# Env overrides for backend iRODS connections (optional)
IRODS_ENV_BACKEND=irods_client_server_negotiation=off,irods_client_server_policy=CS_NEG_REFUSE,irods_ssl_verify_server=none,irods_authentication_scheme=native
# Env overrides for iRODS client config in SODAR (optional)
IRODS_ENV_CLIENT=irods_client_server_negotiation=off,irods_client_server_policy=CS_NEG_REFUSE,irods_ssl_verify_server=none,irods_authentication_scheme=PAM
# Set SSSD auth True if you are using SSSD and PAM
IRODS_SSSD_AUTH=0
# If SSSD/LDAP is not available, you can use internal SODAR auth for iRODS
IRODS_SODAR_AUTH=1
# Host for SODAR auth queries from iRODS if the former value is set true
IRODS_SODAR_API_HOST=http://sodar-web:8080
# Basic auth realm/prompt
SODAR_BASICAUTH_REALM="Please log in with your SODAR user name and password."
#
# SODAR Sample Sheets app settings
#
SODAR_SHEETS_IGV_OMIT_BAM=dragen_evidence.bam
SODAR_SHEETS_IGV_OMIT_VCF=cnv.vcf.gz,ploidy.vcf.gz,sv.vcf.gz
#
# SODAR Landing Zones app settings
#
SODAR_LANDINGZONES_DISABLE_FOR_USERS=0
#
# SODAR Taskflow settings
#
TASKFLOW_LOCK_RETRY_COUNT=2
TASKFLOW_LOCK_RETRY_INTERVAL=3
# iRODS connection timeout for taskflowbackend flows (in seconds)
TASKFLOW_IRODS_CONN_TIMEOUT=960
#
# WebDAV support
#
SODAR_IRODS_WEBDAV_ENABLED=1
SODAR_IRODS_WEBDAV_URL=https://sodar.local
SODAR_IRODS_WEBDAV_URL_ANON=https://sodar.local
SODAR_IRODS_WEBDAV_USER_ANON=ticket
SODAR_IRODS_WEBDAV_IGV_PROXY=0
DAVRODS_VERSION=latest
DAVRODS_ENABLE_TICKETS=1
DAVRODS_AUTH_NAME=Please log in.
#
# Sentry setup (optional)
#
SODAR_ENABLE_SENTRY=0
SODAR_SENTRY_DSN=https://xxx@sentry.host
#
# Postgres credentials
#
# Can remain as they are for docker based deployments
POSTGRES_HOST=postgres
POSTGRES_PORT=5432
POSTGRES_USERNAME=postgres
POSTGRES_PASSWORD=password