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Update galaxy #210

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merged 3 commits into from
Nov 19, 2024
Merged

Update galaxy #210

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18420e3
Update galaxy
micafer Nov 19, 2024
f3fe8d1
Use devel branch
micafer Nov 19, 2024
d1934cc
Use devel branch
micafer Nov 19, 2024
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6 changes: 6 additions & 0 deletions custom_types.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -911,6 +911,11 @@ node_types:
description: Password of the admin user
default: adminpass
required: false
dns_name:
type: string
description: DNS name of the portal
required: false
default: ''
requirements:
- lrms:
capability: tosca.capabilities.indigo.LRMS
Expand All @@ -935,6 +940,7 @@ node_types:
galaxy_admin_password: { get_property: [ SELF, admin_password ] }
galaxy_lrms: { get_property: [ SELF, lrms, type ] }
galaxy_server_name: { get_attribute: [ HOST, private_address, 0 ] }
galaxy_dns_name: { get_property: [ SELF, dns_name ] }

tosca.nodes.indigo.GalaxyWN:
derived_from: tosca.nodes.SoftwareComponent
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17 changes: 14 additions & 3 deletions templates/galaxy.yaml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
tosca_definitions_version: tosca_simple_yaml_1_0

imports:
- grycap_custom_types: https://raw.githubusercontent.com/grycap/tosca/main/custom_types.yaml
- grycap_custom_types: https://raw.githubusercontent.com/grycap/tosca/devel/custom_types.yaml

description: Deploy a Galaxy Server using a local LRMS.

Expand All @@ -28,18 +28,29 @@ topology_template:
description: Password of the Galaxy admin user
default: adminpass

dns_name:
type: string
description: DNS name of the Galaxy portal
default: ''

node_templates:

galaxy_portal:
type: tosca.nodes.indigo.GalaxyPortal
capabilities:
endpoint:
properties:
port: 8443
protocol: tcp
ports:
https:
protocol: tcp
source: 443
http:
protocol: tcp
source: 80
properties:
admin_email: { get_input: admin_email }
admin_password: { get_input: admin_password }
dns_name: { get_input: dns_name }
requirements:
- lrms: local_lrms
- host: simple_node
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2 changes: 1 addition & 1 deletion templates/simple-node-disk.yml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
tosca_definitions_version: tosca_simple_yaml_1_0

imports:
- grycap_custom_types: https://raw.githubusercontent.com/grycap/tosca/main/custom_types.yaml
- grycap_custom_types: https://raw.githubusercontent.com/grycap/tosca/devel/custom_types.yaml

description: >
Deploy a compute node getting the IP and SSH credentials to access via ssh with an extra HD disk.
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2 changes: 1 addition & 1 deletion templates/slurm_cluster.yml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
tosca_definitions_version: tosca_simple_yaml_1_0

imports:
- grycap_custom_types: https://raw.githubusercontent.com/grycap/tosca/main/custom_types.yaml
- grycap_custom_types: https://raw.githubusercontent.com/grycap/tosca/devel/custom_types.yaml

description: Deploy a SLURM Virtual Cluster.

Expand Down
27 changes: 19 additions & 8 deletions templates/slurm_galaxy.yml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
tosca_definitions_version: tosca_simple_yaml_1_0

imports:
- grycap_custom_types: https://raw.githubusercontent.com/grycap/tosca/main/custom_types.yaml
- grycap_custom_types: https://raw.githubusercontent.com/grycap/tosca/devel/custom_types.yaml

description: Deploy a Galaxy portal with an SLURM Virtual Cluster.

Expand All @@ -13,19 +13,24 @@ metadata:
parents:
- slurm_cluster.yml
tabs:
Galaxy Data: admin_.*
Galaxy Data: galaxy_.*

topology_template:
inputs:

admin_email:
galaxy_admin_email:
type: string
description: Email of the Galaxy admin user
default: [email protected]
admin_password:
galaxy_admin_password:
type: string
description: Password of the Galaxy admin user
default: adminpass
galaxy_dns_name:
type: string
description: DNS name of the Galaxy portal
default: ''


slurm_version:
type: string
Expand Down Expand Up @@ -63,11 +68,17 @@ topology_template:
capabilities:
endpoint:
properties:
port: 8443
protocol: tcp
ports:
https:
protocol: tcp
source: 443
http:
protocol: tcp
source: 80
properties:
admin_email: { get_input: admin_email }
admin_password: { get_input: admin_password }
admin_email: { get_input: galaxy_admin_email }
admin_password: { get_input: galaxy_admin_password }
dns_name: { get_input: galaxy_dns_name }
requirements:
- lrms: lrms_front_end
- host: lrms_server
Expand Down
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