usegalaxy-eu · bgruening · Feb 21, 2024 · Feb 21, 2024
diff --git a/templates/galaxy/config/file_sources_conf.yml.j2 b/templates/galaxy/config/file_sources_conf.yml.j2
@@ -236,3 +236,11 @@
   token: ${user.preferences['gitlabfs|read_access_token']}
   server_url: "https://git.nfdi4plants.org"
   writable: true
+
+- type: posix
+  root: '/data/jwd/jbrowse2/'
+  id: jbrowse2_store
+  doc: Storage of JBrowse2 instance for EBP
+  label: EBP JBrowse2
+  requires_groups: ebp-test
+  writable: true
diff --git a/templates/nginx/galaxy-main.j2 b/templates/nginx/galaxy-main.j2
@@ -147,6 +147,10 @@ server {
 		root /opt;
 	}
 
+	location /ebp-jbrowse {
+                alias /data/jwd/jbrowse2;
+                autoindex on;
+        }
 
 	location /static/vgcn {
 		expires 24h;

diff --git a/group_vars/htcondor-secondary-submit-host.yml b/group_vars/htcondor-secondary-submit-host.yml
 nspawn_enable: false
 nspawn_start: false

 nspawn_ssh: yes
 nspawn_ssh_config_path: /etc/ssh/sshd_config
 nspawn_ssh_config:
  Port: "2222"
  rsa: "ssh-rsa-cert-v01@openssh.com AAAAHHNzaC1yc2EtY2VydC12MDFAb3BlbnNzaC5jb20AAAAgQuoZdMdY7Boli6KRlNmUk2zQar66du6kmLR4PkWoHI8AAAADAQABAAABgQDxIgnu5/BIIzVbWM442uzwyuXPQx0jqaVfffjexwewfc2mMNnVAG7mRzcWcgr+o/lFiogkqGulkvO/a+EARs5WsWrsq5bGFcHx9DPgaT+7smu+K3t0WNiqPEykXUJppyMtaYftZSWaCSl51pg3QT29pvl95sjC3URFrQhoaLHJ2fESYJI4WuMBig/rCLaRsF6xaR38LIVfrZdA7UjG5Ncr+FXF6cpNtdvDvJXkGyuYft2p9LMh7vycdiSUL/CluC6tptgQ82JGxgyHDaxwJvyzzDukjKTUkR59ctuGthq9M/M384sCn8Z3PsGE4hkRGdL/HJZhasPIkkwJK8ekucnBR2LzlCqiTrn7HFbndqgePhJWHq0tBN53o2Vmczrbq6UVROAFDCpPKeaWa6hcdqzp0fpHrgSZEyKmMxThV8sj69E/mCh2PEgWjCXsPoJLwrW9TuPUMeXx2+Cwf4/JaFSvLBT19ADFKkzgAPeEVdJg2ZkjWZVO+xxb9e6Ahux+g7EAAAAAAAAAAAAAAAIAAAAVbWFuYWdlci1zZWNvbmRhcnktcnNhAAAAAAAAAABlKAbkAAAAAHfm2ysAAAAAAAAAAAAAAAAAAAEXAAAAB3NzaC1yc2EAAAADAQABAAABAQDLQD6fG38uwFj91GSe6YnRnBuTjXWZN6Pck1JRCTWtufwKV0SZNczD+qUdnFfZrCx/wBVK8R6zL2VWS9hcFK1LuE8HK86f8qG/gcB6yFt/0I/PWoSjcbUMPQTzFIy8yxvdIoPTlj/P6+uNgweTvMFI4+UOuCI71IhB/liTHn1/2dXQM94SFd4VQeg+3Tc6gDxEqRSS6dLIq0uvR8//luIpoW38yh2ozwHmjMKTvHnbduGqHlES4qz9cU9iZkWoPzSp+qoxCOijHvwzL5vD0/k4hZ/iJyTzDHQLDra3Kaa8ykWdERCxjpMp1y9dVQ23lVxp+UUAt3RHOCU1/KuNM9PrAAABFAAAAAxyc2Etc2hhMi01MTIAAAEAOXRiZFs14HScCvi+9Hp51z310t0r3SHtHhE50vEjdAsnej+/yHUtlmaYJ1l4B8SWYHHUV94KxZbQP79D8PYQextXoYldA4Vp29ow33sYF8Mr4p7Jbjyyr4GVP9RAymiZz9cuiiRqjs8qwn/UCOw4A6yaix4k0EYTJa9bpbD3MsCxJbKEdZxxL72kIKf4sGuDrd77hEtRwJFUSqz+XD96TYG+BIomnrk35Oy+oyMGhoIlSM0//cS0pHUW8fpGnRIJJbBjDETwOmaMEF5yynRSeJyWnEBPpjcA+1i7wILSxYxZb5ckGxCABYxNvlIhF8Bvdcyb4eo7B/WeEdzr5C+Pzg== /etc/ssh/ssh_host_rsa_key.pub"
 nspawn_ssh_authorized_keys:
  - "ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAACAQDV7gfNbNN5O8vH6/tM/iOFXKBP2YKRHXOmdfV8ogvu9BdVV0IPmDzk2EooVpThDE1VMv1hz3811tvBhHRJ6IgNhVIV/61w/+RazQD/AU27X8bX+Hb9EQ/bP4DW+6ySd/z5vdDLzpH5dbiMhzPEDkXVsylUT+hkQnas6cHspDhHmtKQ5MWOgDe3D/IEudTDJQe8hxxaU4TaZUmFzn7eYp9HvuK8qW0yCy4NWOxJJHA+G5wSCyLuKnaKo4AitUIzSKF1AB94oq7b96KONhPxgRptAk4OYIUTdNFbrI5HDaSNzHLnF5FbjQvG+Eu6m5nY5yvJMogE+jiuWeIXCZTCFljg287FUo0ohmbZpd802L6VXun14VumRC+rRgPrvBALo/CsyCsPIoBSTKhVElxKVOcRjmTLNfrUZM0GQxqJhIvah8BV+JTExkipPwkrKTdMAWIXvCoehxV+WMpBWqtEEzAzEoqJpaiec7HfriwsHTGESZWAPYEbFjzbHXQZtqBkbOvtokPMRmTWfWKxaplCMN6ddJeeY6faorD0w/e6lszWES1Q1ieajiPKDy37UvybKKvPTk4o3MzyzYOS4c8HQj+jnGeR5Q3ETuyz4psLyOfuBtIrfOeuxV42rFDmkYM3IrrRR+F9oklFG6Ig8DVfgQEzSG36NkgvpF4OdFvigYqXvw== cloud@vgcn"
 nspawn_ssh_host_trust_container: yes

 nspawn_condor_systemd_run: "/usr/bin/systemd-run -p EnvironmentFile={{ nspawn_galaxy_environment_file }} --uid={{ galaxy_user.uid }} --gid={{ galaxy_group.gid }} --pipe --quiet --machine {{ nspawn_name }}"
 nspawn_condor_rm_command: "{{ nspawn_condor_systemd_run }} /usr/bin/condor_rm"
diff --git a/group_vars/htcondor/vault.yml b/group_vars/htcondor/vault.yml
 $ANSIBLE_VAULT;1.1;AES256
 36336166336332656436376537343036353234366164616236393139313932343538313133373639
 3064333637333539353566396361666362666539353231360a646430356366343632633637326462
 39333232646363656438316533666664613935353336313064323038313564383734373433656330
diff --git a/group_vars/htcondor-secondary/vault.yml b/group_vars/htcondor-secondary/vault.yml
 $ANSIBLE_VAULT;1.1;AES256
 31353533313831356632376636636564653732313930623263376437313362386632623732306136
 3465326632326138646330353164336363653764396237370a393562613834343765313835656362
 66633030353534663831323939386335316130343137396139633038366438613731376130663564
diff --git a/files/clouds.yaml b/files/clouds.yaml
 $ANSIBLE_VAULT;1.1;AES256
 35653765643938363737613233643036373566633739313036346366393862363733346630653732
 6131353838333839646330336663353136323766396537300a373033626639393332663939653165
 33376130313031333232383364313033656333613638663836623930326537613531663138306536
diff --git a/files/galaxy/tpv/tool_defaults.yml b/files/galaxy/tpv/tool_defaults.yml
          Invalid 'Remote resources id' selected in the config menu under 'User -> Preferences -> Manage Information -> Use distributed compute resources'. Please reselect either 'default' or an appropriate remote resource then click 'Save' and rerun your job.
      - id: secondary_cluster
        # Send all jobs to the secondary HTCondor cluster.
        if: True
        execute: |
          from tpv.core.entities import Tag, TagSetManager, TagType

diff --git a/files/galaxy/subdomains/assembly/themes/assembly.yml b/files/galaxy/subdomains/assembly/themes/assembly.yml
 assembly:
  masthead:
    color: >
      bottom -90px left / 1000px no-repeat url("/static/dist/flying-bird-1.svg"),
diff --git a/files/galaxy/subdomains/singlecell/themes/singlecell.yml b/files/galaxy/subdomains/singlecell/themes/singlecell.yml
 singlecell:
  masthead:
    color: "#530080"
diff --git a/files/galaxy/subdomains/annotation/themes/annotation.yml b/files/galaxy/subdomains/annotation/themes/annotation.yml
 annotation:
  masthead:
    color: >
      linear-gradient(to right, #3337 0, #3337 365px, transparent 365px),
diff --git a/files/galaxy/subdomains/plants/themes/plants.yml b/files/galaxy/subdomains/plants/themes/plants.yml
 plants:
  masthead:
    color: >
      linear-gradient(90deg,
	nspawn_enable: false
	nspawn_start: false

	nspawn_ssh: yes
Check warning on line 49 in group_vars/htcondor-secondary-submit-host.yml GitHub Actions / Lint `49:13 [truthy] truthy value should be one of [false, true]`
	nspawn_ssh_config_path: /etc/ssh/sshd_config
	nspawn_ssh_config:
	Port: "2222"
	rsa: "ssh-rsa-cert-v01@openssh.com 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 /etc/ssh/ssh_host_rsa_key.pub"
	nspawn_ssh_authorized_keys:
	- "ssh-rsa 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 cloud@vgcn"
	nspawn_ssh_host_trust_container: yes
Check warning on line 77 in group_vars/htcondor-secondary-submit-host.yml GitHub Actions / Lint `77:34 [truthy] truthy value should be one of [false, true]`

	nspawn_condor_systemd_run: "/usr/bin/systemd-run -p EnvironmentFile={{ nspawn_galaxy_environment_file }} --uid={{ galaxy_user.uid }} --gid={{ galaxy_group.gid }} --pipe --quiet --machine {{ nspawn_name }}"
	nspawn_condor_rm_command: "{{ nspawn_condor_systemd_run }} /usr/bin/condor_rm"
	$ANSIBLE_VAULT;1.1;AES256
Check warning on line 1 in group_vars/htcondor/vault.yml GitHub Actions / Lint `1:1 [document-start] missing document start "---"`
	36336166336332656436376537343036353234366164616236393139313932343538313133373639
	3064333637333539353566396361666362666539353231360a646430356366343632633637326462
	39333232646363656438316533666664613935353336313064323038313564383734373433656330
	$ANSIBLE_VAULT;1.1;AES256
Check warning on line 1 in group_vars/htcondor-secondary/vault.yml GitHub Actions / Lint `1:1 [document-start] missing document start "---"`
	31353533313831356632376636636564653732313930623263376437313362386632623732306136
	3465326632326138646330353164336363653764396237370a393562613834343765313835656362
	66633030353534663831323939386335316130343137396139633038366438613731376130663564
	$ANSIBLE_VAULT;1.1;AES256
Check warning on line 1 in files/clouds.yaml GitHub Actions / Lint `1:1 [document-start] missing document start "---"`
	35653765643938363737613233643036373566633739313036346366393862363733346630653732
	6131353838333839646330336663353136323766396537300a373033626639393332663939653165
	33376130313031333232383364313033656333613638663836623930326537613531663138306536
	Invalid 'Remote resources id' selected in the config menu under 'User -> Preferences -> Manage Information -> Use distributed compute resources'. Please reselect either 'default' or an appropriate remote resource then click 'Save' and rerun your job.
	- id: secondary_cluster
	# Send all jobs to the secondary HTCondor cluster.
	if: True
Check warning on line 65 in files/galaxy/tpv/tool_defaults.yml GitHub Actions / Lint `65:13 [truthy] truthy value should be one of [false, true]`
	execute: \|
	from tpv.core.entities import Tag, TagSetManager, TagType
	assembly:
Check warning on line 1 in files/galaxy/subdomains/assembly/themes/assembly.yml GitHub Actions / Lint `1:1 [document-start] missing document start "---"`
	masthead:
	color: >
	bottom -90px left / 1000px no-repeat url("/static/dist/flying-bird-1.svg"),
	singlecell:
Check warning on line 1 in files/galaxy/subdomains/singlecell/themes/singlecell.yml GitHub Actions / Lint `1:1 [document-start] missing document start "---"`
	masthead:
	color: "#530080"
	annotation:
Check warning on line 1 in files/galaxy/subdomains/annotation/themes/annotation.yml GitHub Actions / Lint `1:1 [document-start] missing document start "---"`
	masthead:
	color: >
	linear-gradient(to right, #3337 0, #3337 365px, transparent 365px),
	plants:
Check warning on line 1 in files/galaxy/subdomains/plants/themes/plants.yml GitHub Actions / Lint `1:1 [document-start] missing document start "---"`
	masthead:
	color: >
	linear-gradient(90deg,