Analyse des Génomes 2024 -- Checkpoint 2 #40

drosofff · 2024-11-13T17:36:07Z

drosofff
Nov 13, 2024
Maintainer

Checking proper deployment of the Galaxy Server

After your Galaxy server deployment, the log at your screen as well as the last lines of /root//install_log.txt should show :

changed: [localhost] => (item={'name': 'sambamba', 'owner': 'artbio', 'tool_panel_section_id': 'samtools', 'tool_panel_section_label': 'Samtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})
changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Wed Nov 13 18:05:40 UTC 2024
-- Installation is complete --

Type the following command in the web ssh terminal of your Google VM.

galaxyctl status

⚠️ You must have the sudo right to execute properly this command (ie sudo -i is not already done)

Check points 1. and 2. and post your results here (⚠️ no screenshot) in a separate comment (one by student)

drosofff · 2024-11-16T17:12:30Z

drosofff
Nov 16, 2024
Maintainer Author

changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Mon Nov 18 09:25:10 UTC 2024
-- Installation is complete --

and

root@galaxy-image-2024-11-18:~# galaxyctl status
  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

0 replies

Baptiste-Dm · 2024-11-23T15:12:16Z

Baptiste-Dm
Nov 23, 2024

Bonjour,

Voici les dernières lignes de mon installation du serveur Galaxy:

changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Sat Nov 23 14:46:39 UTC 2024
-- Installation is complete --

et voici le statut du serveur Galaxy:

root@ansible-galaxy:~# galaxyctl status
  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

1 reply

drosofff Nov 24, 2024
Maintainer Author

🎉 🥇 Vous marquez aussi le point de la deuxième manche @Baptiste-Dm !

mhully · 2024-11-23T17:23:12Z

mhully
Nov 23, 2024

Bonjour, voici les informations pour l'étape 2 :

changed: [localhost] => (item={'name': 'sambamba', 'owner': 'artbio', 'tool_panel_section_id': 'samtools', 'tool_panel_section_label': 'Samtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})
changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Sat Nov 23 17:17:00 UTC 2024
-- Installation is complete --

et :

root@ansible-galaxy:~# galaxyctl status
  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

1 reply

slecrom Nov 24, 2024
Collaborator

Merci @mhully Vous êtes prêt pour la dernière étape.

YoannGS · 2024-11-23T17:25:54Z

YoannGS
Nov 23, 2024

Bonjour,
Voici les dernières lignes de l'installation :

changed: [localhost] => (item={'name': 'sambamba', 'owner': 'artbio', 'tool_panel_section_id': 'samtools', 'tool_panel_section_label': 'Samtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})
changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})
...ignoring

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=1   

Sat Nov 23 17:08:50 UTC 2024
-- Installation is complete --

et le statut du serveur :

root@ansible-galaxy:~# galaxyctl status
  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

1 reply

slecrom Nov 24, 2024
Collaborator

Parfait @YoannGS prêt pour la suite.

Emmabenbakir · 2024-11-24T11:02:44Z

Emmabenbakir
Nov 24, 2024

Bonjour, voici les informations pour l'étape 2:

changed: [localhost] => (item={'name': 'sambamba', 'owner': 'artbio', 'tool_panel_section_id': 'samtools', 'tool_panel_section_label': 'Samtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})
changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Sun Nov 24 10:41:33 UTC 2024
-- Installation is complete -- ```

et :

UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
 galaxy-celery-beat.service loaded active running Galaxycelery-beat        
 galaxy-celery.service      loaded active running Galaxycelery             
 galaxy-gunicorn.service    loaded active running Galaxygunicorn           
 galaxy-handler0.service    loaded active running Galaxyhandler0           
 galaxy-handler1.service    loaded active running Galaxyhandler1           
 [email protected]   loaded active running Galaxyhandler (process 0)
 [email protected]   loaded active running Galaxyhandler (process 1)
 galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

1 reply

slecrom Nov 24, 2024
Collaborator

Bonsoir @Emmabenbakir
Votre serveur Galaxy fonctionne. Quand vous collez le contenu d'un terminal, utilisez l'icône "<>" de la barre de l'éditeur. Le résultat est plus lisible.
Merci

sarah-grn · 2024-11-24T12:17:36Z

sarah-grn
Nov 24, 2024

Bonjour,

Mon ordinateur s'est mis en veille pendant l'installation du serveur Galaxy, voici les dernières lignes de mon installation (via commande tail -f /root/install_log.txt) : Est ce que c'est bien OK?

root@ansible-galaxy:~# tail -f /root/install_log.txt
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Sun Nov 24 11:19:26 UTC 2024
-- Installation is complete --

et le statut du serveur Galaxy:

root@ansible-galaxy:~# galaxyctl status
  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

2 replies

slecrom Nov 24, 2024
Collaborator

Bonsoir @sarah-grn
L'installation s'est bien passée. @drosofff a utilisé un système de déploiement qui permet de se protéger d'une partie des risques de déconnexion.
Bonne soirée.

drosofff Nov 24, 2024
Maintainer Author

🛌 😴 Pas grave @sarah-grn , même les ordinateurs ont le droit de dormir 😄

MichielTaw · 2024-11-24T15:12:39Z

MichielTaw
Nov 24, 2024

Bonjour, voici les output:

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Sun Nov 24 14:22:52 UTC 2024
-- Installation is complete --

root@ansible-galaxy:~# galaxyctl status
  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

1 reply

slecrom Nov 24, 2024
Collaborator

Merci @MichielTaw tout est bon. Bonne soirée.

n-lacombe · 2024-11-24T20:39:12Z

n-lacombe
Nov 24, 2024

Voici les dernières lignes de l'installation du serveur Galaxy :

changed: [localhost] => (item={'name': 'sambamba', 'owner': 'artbio', 'tool_panel_section_id': 'samtools', 'tool_panel_section_label': 'Samtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})
ok: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=4    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Sun Nov 24 12:09:25 UTC 2024
-- Installation is complete --

Le statut de serveur :

root@ansible-galaxy:~# galaxyctl status
  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1                  
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

1 reply

slecrom Nov 25, 2024
Collaborator

Bonjour @n-lacombe
L'installation de votre serveur Galaxy est terminée. Vous êtes prêt pour la dernière étape.
Bonne journée.

LoannPtr · 2024-11-24T20:47:17Z

LoannPtr
Nov 24, 2024

Je pense que l'installation s'est mal passé pour moi vu que les dernières lignes ne sont pas les mêmes.

PLAY RECAP *********************************************************************
localhost : ok=3 changed=0 unreachable=0 failed=1 skipped=1 rescued=0 ignored=0

Fri Nov 22 20:29:27 UTC 2024
-- Installation is complete --

8 replies

LoannPtr Nov 25, 2024

Je tiens aussi à préciser que j'ai réalisé l'installation une première fois mais ma connexion a sauté donc j'ai réessayé et obtenu ce fichier.

LoannPtr Nov 26, 2024

Après avoir fait une nouvelle VM, c'est bon:

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost : ok=11 changed=5 unreachable=0 failed=0 skipped=3 rescued=0 ignored=0

drosofff Nov 26, 2024
Maintainer Author

OK @LoannPtr , la raison pour laquelle le premier déploiement a échoué n'est pas très claire. Ce n'est pas parce que la connexion a sauté en tout cas. Mais on est d'accord qu'on ne va pas faire une thèse sur la question.

LoannPtr Nov 27, 2024

Et voici le statut de galaxy associé

root@vm-ag-2:~# galaxyctl status
UNIT LOAD ACTIVE SUB DESCRIPTION
galaxy-celery-beat.service loaded active running Galaxycelery-beat
galaxy-celery.service loaded active running Galaxycelery
galaxy-gunicorn.service loaded active running Galaxygunicorn
galaxy-handler0.service loaded active running Galaxyhandler0
galaxy-handler1.service loaded active running Galaxyhandler1
[email protected] loaded active running Galaxyhandler (process 0)
[email protected] loaded active running Galaxyhandler (process 1)
galaxy.target loaded active active Galaxy

LOAD = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

slecrom Nov 27, 2024
Collaborator

Merci @LoannPtr vous pouvez passer à la dernière étape.

Nicolas-Doucet · 2024-11-25T10:02:35Z

Nicolas-Doucet
Nov 25, 2024

j'ai un soucis :
nicolas_doucet24@ansible-galaxy:$ galaxyctl status
galaxyctl: command not found
nicolas_doucet24@ansible-galaxy:$ tail -f ~/install_log.txt
Mon Nov 25 08:48:16 UTC 2024
-- Installation is complete --
Mon Nov 25 09:00:28 UTC 2024
Reading package lists...
Mon Nov 25 09:02:24 UTC 2024
-- Installation is complete --
Mon Nov 25 09:12:41 UTC 2024
Reading package lists...
Mon Nov 25 09:14:36 UTC 2024
-- Installation is complete --
le téléchargement ce bloque à ce stade là sans raison. Il continue pendant plusieurs heures comme ça et cela indépendamment de la machine sur laquelle je réalise le téléchargement

7 replies

Nicolas-Doucet Nov 25, 2024

Quel téléchargement @Nicolas-Doucet ?

l'installation de galaxy (pour l'ip je ne peux pas la donner tout de suite)

slecrom Nov 25, 2024
Collaborator

@drosofff je pense que @Nicolas-Doucet fait référence à celui des packages d'installation de la machine galaxy.

Nicolas-Doucet Nov 25, 2024

Si votre machine est active, merci de m'indiquer son adresse IP dans le Slack @Nicolas-Doucet

vous voulez l'adresse IP interne ou externe ?

drosofff Nov 25, 2024
Maintainer Author

Externe.
Quand vous hésitez entre deux informations, donnez-les toutes les deux 😄

drosofff Nov 25, 2024
Maintainer Author

DANS LE SLACK !

sbensous · 2024-11-25T12:07:04Z

sbensous
Nov 25, 2024

Voici pour l'étape 2 (Samuel Bensoussan)
``root@ansible-galaxy:~# galaxyctl status
UNIT LOAD ACTIVE SUB DESCRIPTION
galaxy-celery-beat.service loaded active running Galaxycelery-beat
galaxy-celery.service loaded active running Galaxycelery
galaxy-gunicorn.service loaded active running Galaxygunicorn
galaxy-handler0.service loaded active running Galaxyhandler0
galaxy-handler1.service loaded active running Galaxyhandler1
[email protected] loaded active running Galaxyhandler (process 0)
[email protected] loaded active running Galaxyhandler (process 1)
galaxy.target loaded active active Galaxy

LOAD = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.
root@ansible-galaxy:~# ``

Je n'ai pas compris comment faire comprendre à github qu'une partie de mon message est du code malgré l'ajout de <>

4 replies

slecrom Nov 25, 2024
Collaborator

Merci @sbensous Pouvez-vous aussi coller le résultat de la commande tail -f ~/install_log.txt en utilisant la mise en forme du code dans la barre de l'éditeur de texte "<>" ?

slecrom Nov 25, 2024
Collaborator

Vous pouvez-utiliser le symbole ``` en début et en fin des lignes de codes.

slecrom Nov 25, 2024
Collaborator

Exemple :

Ceci est du code

sbensous Nov 25, 2024

Merci @sbensous Pouvez-vous aussi coller le résultat de la commande tail -f ~/install_log.txt en utilisant la mise en forme du code dans la barre de l'éditeur de texte "<>" ?

voici :

root@ansible-galaxy:~# tail -f ~/install_log.txt
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Mon Nov 25 11:49:03 UTC 2024
-- Installation is complete -- ```

sbensous · 2024-11-25T12:10:25Z

sbensous
Nov 25, 2024

test code

0 replies

sbensous · 2024-11-25T12:10:36Z

sbensous
Nov 25, 2024

  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.
root@ansible-galaxy:~# ```

2 replies

sbensous Nov 25, 2024

c'est bon, c'est compris

slecrom Nov 25, 2024
Collaborator

Merci @sbensous vous pouvez passer à la dernière étape

alleongaelle · 2024-11-25T12:40:55Z

alleongaelle
Nov 25, 2024

Voici pour l'étape 2 :
Partie 1:

changed: [localhost] => (item={'name': 'sambamba', 'owner': 'artbio', 'tool_panel_section_id': 'samtools', 'tool_panel_section_label': 'Samtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})
changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Mon Nov 25 12:30:56 UTC 2024
-- Installation is complete --

Partie 2:

root@instance-20241125-111151:~# galaxyctl status
  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

1 reply

slecrom Nov 25, 2024
Collaborator

Parfait @alleongaelle vous êtes prête pour la dernière étape.

Nicolas-Doucet · 2024-11-25T12:54:40Z

Nicolas-Doucet
Nov 25, 2024

Normalement` maintenant c'est bon :

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Mon Nov 25 12:48:09 UTC 2024
-- Installation is complete --

UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy

   LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'

2 replies

slecrom Nov 25, 2024
Collaborator

Merci @Nicolas-Doucet vous pouvez passer à la dernière étape. Comment avez-vous fait pour résoudre votre problème d'installation ?

drosofff Nov 25, 2024
Maintainer Author

Il a suivi les instructions de la documentation 😉

Maille0 · 2024-11-25T17:50:19Z

Maille0
Nov 25, 2024

Grégoire Blavier

1ère partie

changed: [localhost] => (item={'name': 'sambamba', 'owner': 'artbio', 'tool_panel_section_id': 'samtools', 'tool_panel_section_label': 'Samtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})
changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Mon Nov 25 17:47:23 UTC 2024
-- Installation is complete --

2nde partie

root@ansible-galaxy:~# galaxyctl status
  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

1 reply

slecrom Nov 26, 2024
Collaborator

Merci @Maille0 votre serveur Galaxy est prêt. Vous pouvez passer à la dernière étape.

fabouraima · 2024-11-25T18:07:04Z

fabouraima
Nov 25, 2024

faroukbouraima@ansible-galaxy:~$ tail -f ~/install_log.txt
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost : ok=11 changed=3 unreachable=0 failed=0 skipped=3 rescued=0 ignored=0

Mon Nov 25 17:52:26 UTC 2024
-- Installation is complete --
UNIT LOAD ACTIVE SUB DESCRIPTION
galaxy-celery-beat.service loaded active running Galaxycelery-beat
galaxy-celery.service loaded active running Galaxycelery
galaxy-gunicorn.service loaded active running Galaxygunicorn
galaxy-handler0.service loaded active running Galaxyhandler0
galaxy-handler1.service loaded active running Galaxyhandler1
[email protected] loaded active running Galaxyhandler (process 0)
[email protected] loaded active running Galaxyhandler (process 1)
galaxy.target loaded active active Galaxy

LOAD = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.
root@ansible-galaxy:~#

1 reply

slecrom Nov 26, 2024
Collaborator

Bonjour @fabouraima

Pouvez-vous également coller la sortie de la commande galaxyctl status en l'entourant de ``` pour afficher le code plus clairement ?

MercI

MathildeQuib · 2024-11-25T19:41:08Z

MathildeQuib
Nov 25, 2024

Bonsoir,
Dernières lignes de l'installation

changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Mon Nov 25 19:16:45 UTC 2024
-- Installation is complete --```

And

```root@ansible-galaxy-20241122-152827:~# galaxyctl status
  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.```

2 replies

MathildeQuib Nov 25, 2024

Il me manquait une ligne dans mon commentaire précédent par rapport au modèle demandé pour les dernières lignes de l'installation :

changed: [localhost] => (item={'name': 'sambamba', 'owner': 'artbio', 'tool_panel_section_id': 'samtools', 'tool_panel_section_label': 'Samtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})
changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Mon Nov 25 19:16:45 UTC 2024
-- Installation is complete --

slecrom Nov 26, 2024
Collaborator

Merci @MathildeQuib tout est bon. Vous êtes prête pour la dernière étape.

oceanewthr · 2024-11-25T21:08:11Z

oceanewthr
Nov 25, 2024

Partie 1 :

changed: [localhost] => (item={'name': 'sambamba', 'owner': 'artbio', 'tool_panel_section_id': 'samtools', 'tool_panel_section_label': 'Samtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})
changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Mon Nov 25 20:55:19 UTC 2024
-- Installation is complete --

Partie 2 :

  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

1 reply

slecrom Nov 26, 2024
Collaborator

Bonjour @oceanewthr

Parfait merci. J'annonce la dernière étape ce matin dans Slack.

Pirhhot · 2024-11-26T08:22:03Z

Pirhhot
Nov 26, 2024

Bonjour,

quand je regarde les logs d'installation je trouve bien la ligne :
Tue Nov 26 08:16:10 UTC 2024 -- Installation is complete --

Cependant, en essayant la commande de test, je reçois l'erreur :
Error: Invalid value for '-c' / '--config-file': File '/home/galaxy/galaxy/config/galaxy.yml' does not exist.

7 replies

drosofff Nov 26, 2024
Maintainer Author

Alors @Pirhhot ?

Pirhhot Nov 28, 2024

Effectivement, le problème provenait de sudo -i

j'obtiens

root@ansible-galaxy:~# galaxyctl status
UNIT LOAD ACTIVE SUB DESCRIPTION
galaxy-celery-beat.service loaded active running Galaxycelery-beat
galaxy-celery.service loaded active running Galaxycelery
galaxy-gunicorn.service loaded active running Galaxygunicorn
galaxy-handler0.service loaded active running Galaxyhandler0
galaxy-handler1.service loaded active running Galaxyhandler1
[[email protected]](mailto:[email protected]) loaded active running Galaxyhandler (process 0)
[[email protected]](mailto:[email protected]) loaded active running Galaxyhandler (process 1)
galaxy.target loaded active active Galaxy

LOAD = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

slecrom Nov 28, 2024
Collaborator

Merci @Pirhhot Pouvez-vous aussi nous donner le résultat de la commande tail -f ~/install_log.txt ?

Pirhhot Nov 28, 2024

root@ansible-galaxy:~# tail -f ~/install_log.txt
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Mon Nov 25 13:18:56 UTC 2024
-- Installation is complete --

slecrom Nov 28, 2024
Collaborator

Parfait merci. L'installation, c'est bien passée. Vous êtes prêt pour la dernière étape.

Juleslr22 · 2024-11-26T08:50:12Z

Juleslr22
Nov 26, 2024

Bonjour, voici mes infos pour l'étape 2 :

changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Tue Nov 26 08:43:49 UTC 2024
-- Installation is complete --

et :

  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.```

1 reply

slecrom Nov 26, 2024
Collaborator

Merci @Juleslr22 il ne vous reste plus qu'à effectuer la dernière étape.

ldebarbarin · 2024-11-26T15:33:48Z

ldebarbarin
Nov 26, 2024

Bonjour,
Voici mon output:

root@ansible-galaxy:~# galaxyctl status
  UNIT                       LOAD   ACTIVE SUB     DESCRIPTION              
  galaxy-celery-beat.service loaded active running Galaxycelery-beat        
  galaxy-celery.service      loaded active running Galaxycelery             
  galaxy-gunicorn.service    loaded active running Galaxygunicorn           
  galaxy-handler0.service    loaded active running Galaxyhandler0           
  galaxy-handler1.service    loaded active running Galaxyhandler1           
  [email protected]   loaded active running Galaxyhandler (process 0)
  [email protected]   loaded active running Galaxyhandler (process 1)
  galaxy.target              loaded active active  Galaxy                   

LOAD   = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB    = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.

1 reply

slecrom Nov 26, 2024
Collaborator

Bonjour @ldebarbarin
Merci pour le partage de l'état du serveur. Pourriez-vous aussi partager la sortie de la commande tail -f ~/install_log.txt ?
Merci

ldebarbarin · 2024-11-26T16:39:26Z

ldebarbarin
Nov 26, 2024

Oui bien sûr,
Voici:

root@ansible-galaxy:~# tail -f ~/install_log.txt
skipping: [localhost]

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost                  : ok=11   changed=5    unreachable=0    failed=0    skipped=3    rescued=0    ignored=0   

Mon Nov 25 13:22:13 UTC 2024
-- Installation is complete --

6 replies

ldebarbarin Nov 26, 2024

Existe t'il une commande particulière à réaliser afin de récupérer le document pour vous le déposer ?
Je vous remercie,
Luna

ldebarbarin Nov 26, 2024

Par ailleurs, j'ai remarqué que sur toutes les copies d'écran partagées, il y'a "skipped=3" :)

drosofff Nov 26, 2024
Maintainer Author

Le plus simple, c'est d'entrer les commandes suivantes (considérant que vous êtes root sudo -i)

clear
cat /root/install_log.txt

Maintenant vous copiez la totalité du terminal web, et vous le collez ici, en n’oubliant pas de le formater entre deux blocs ``` seuls sur leur lignes avant et après.

drosofff Nov 26, 2024
Maintainer Author

Mais, désolé, et au temps pour moi: Les étapes "skipped" le sont normalement. Il n'y a pas de soucis, j'ai aboyé trop vite.

slecrom Nov 27, 2024
Collaborator

Bonjour @ldebarbarin
Tout est donc bon pour cette étape. Vous pouvez passer au chargement des données.
Bonne journée

Enzobcrl · 2024-11-26T23:31:02Z

Enzobcrl
Nov 26, 2024

changed: [localhost] => (item={'name': 'sambamba', 'owner': 'artbio', 'tool_panel_section_id': 'samtools', 'tool_panel_section_label': 'Samtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})
changed: [localhost] => (item={'name': 'bedtools', 'owner': 'iuc', 'tool_panel_section_id': 'bedtools', 'tool_panel_section_label': 'Bedtools', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu/'})

TASK [install.galaxy-tools : include_tasks] ************************************
skipping: [localhost]

PLAY RECAP *********************************************************************
localhost : ok=11 changed=5 unreachable=0 failed=0 skipped=3 rescued=0 ignored=0

Tue Nov 26 23:27:09 UTC 2024
-- Installation is complete --

2 replies

Enzobcrl Nov 26, 2024

UNIT LOAD ACTIVE SUB DESCRIPTION
galaxy-celery-beat.service loaded active running Galaxycelery-beat
galaxy-celery.service loaded active running Galaxycelery
galaxy-gunicorn.service loaded active running Galaxygunicorn
galaxy-handler0.service loaded active running Galaxyhandler0
galaxy-handler1.service loaded active running Galaxyhandler1
[email protected] loaded active running Galaxyhandler (process 0)
[email protected] loaded active running Galaxyhandler (process 1)
galaxy.target loaded active active Galaxy

LOAD = Reflects whether the unit definition was properly loaded.
ACTIVE = The high-level unit activation state, i.e. generalization of SUB.
SUB = The low-level unit activation state, values depend on unit type.

8 loaded units listed.
To show all installed unit files use 'systemctl list-unit-files'.
root@ansible-galaxy:~#

slecrom Nov 27, 2024
Collaborator

Bonjour @Enzobcrl
Merci pour le partage de vos logs. Votre serveur Galaxy est installé, vous pouvez passer à la dernière étape et charger vos données.
Bonne journée

Analyse des Génomes 2024 -- Checkpoint 2 #40

drosofff Nov 13, 2024 Maintainer

Checking proper deployment of the Galaxy Server

Check points 1. and 2. and post your results here (⚠️ no screenshot) in a separate comment (one by student)

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