Checking the deployment of your Galaxy server #29

drosofff · 2023-11-21T00:13:46Z

drosofff
Nov 21, 2023
Maintainer

After your Galaxy server deployment, please paste (paste is not a screenshot) the result of the command:

systemctl status galaxy*.service

in the web console of your Google VM.

CoralineBernachot · 2023-11-27T09:07:13Z

CoralineBernachot
Nov 27, 2023

●  galaxy-celery.service - Galaxy celery                                                                        
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)              
     Active: active (running) since Mon 2023-11-27 08:55:54 UTC; 2min 34s ago                                  
   Main PID: 6247 (celery)                                                                                     
      Tasks: 2 (limit: 38496)                                                                                  
     Memory: 193.5M                                                                                            
        CPU: 6.019s                                                                                            
     CGroup: /system.slice/galaxy-celery.service                                                               
             ├─6247 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker --c>
             └─6284 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main(7)

Nov 27 08:55:59 bare-galaxy galaxyctl[6247]: [2023-11-27 08:55:59,645: INFO/MainProcess] Connected to sqlalche>
Nov 27 08:55:59 bare-galaxy galaxyctl[6247]: [2023-11-27 08:55:59,645: DEBUG/MainProcess] ^-- substep ok
Nov 27 08:55:59 bare-galaxy galaxyctl[6247]: [2023-11-27 08:55:59,645: DEBUG/MainProcess] | Consumer: Starting>
Nov 27 08:55:59 bare-galaxy galaxyctl[6247]: [2023-11-27 08:55:59,645: DEBUG/MainProcess] ^-- substep ok
Nov 27 08:55:59 bare-galaxy galaxyctl[6247]: [2023-11-27 08:55:59,645: DEBUG/MainProcess] | Consumer: Starting>
Nov 27 08:55:59 bare-galaxy galaxyctl[6247]: [2023-11-27 08:55:59,645: DEBUG/MainProcess] ^-- substep ok
Nov 27 08:55:59 bare-galaxy galaxyctl[6247]: [2023-11-27 08:55:59,645: DEBUG/MainProcess] | Consumer: Starting>
Nov 27 08:55:59 bare-galaxy galaxyctl[6247]: [2023-11-27 08:55:59,731: DEBUG/MainProcess] ^-- substep ok
Nov 27 08:55:59 bare-galaxy galaxyctl[6247]: [2023-11-27 08:55:59,731: DEBUG/MainProcess] | Consumer: Starting>
Nov 27 08:55:59 bare-galaxy galaxyctl[6247]: [2023-11-27 08:55:59,731: INFO/MainProcess] celery@bare-galaxy re>

● galaxy-celery-beat.service - Galaxy celery-beat
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)
     Active: active (running) since Mon 2023-11-27 08:55:54 UTC; 2min 34s ago
   Main PID: 6246 (celery)
      Tasks: 1 (limit: 38496)
     Memory: 185.2M
        CPU: 4.596s
     CGroup: /system.slice/galaxy-celery-beat.service
             └─6246 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat --log>

Nov 27 08:55:59 bare-galaxy galaxyctl[6246]: [2023-11-27 08:55:59,564: DEBUG/MainProcess] Setting default sock>
Nov 27 08:55:59 bare-galaxy galaxyctl[6246]: [2023-11-27 08:55:59,564: INFO/MainProcess] beat: Starting...
Nov 27 08:55:59 bare-galaxy galaxyctl[6246]: [2023-11-27 08:55:59,604: DEBUG/MainProcess] Current schedule:
Nov 27 08:55:59 bare-galaxy galaxyctl[6246]: <ScheduleEntry: prune-history-audit-table galaxy.prune_history_au>
Nov 27 08:55:59 bare-galaxy galaxyctl[6246]: <ScheduleEntry: clean-object-store-caches galaxy.clean_object_sto>
Nov 27 08:55:59 bare-galaxy galaxyctl[6246]: <ScheduleEntry: cleanup-expired-notifications galaxy.cleanup_expi>
Nov 27 08:55:59 bare-galaxy galaxyctl[6246]: <ScheduleEntry: cleanup-short-term-storage galaxy.cleanup_short_t>
Nov 27 08:55:59 bare-galaxy galaxyctl[6246]: <ScheduleEntry: celery.backend_cleanup celery.backend_cleanup() <>
Nov 27 08:55:59 bare-galaxy galaxyctl[6246]: [2023-11-27 08:55:59,605: DEBUG/MainProcess] beat: Ticking with m>
Nov 27 08:55:59 bare-galaxy galaxyctl[6246]: [2023-11-27 08:55:59,608: DEBUG/MainProcess] beat: Waking up in 5>

● galaxy-gunicorn.service - Galaxy gunicorn
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)
     Active: active (running) since Mon 2023-11-27 08:55:54 UTC; 2min 34s ago
   Main PID: 6248 (gunicorn)
      Tasks: 14 (limit: 38496)
     Memory: 464.3M
        CPU: 20.258s
     CGroup: /system.slice/galaxy-gunicorn.service
             ├─6248 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_f>
             └─6286 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_f>

Nov 27 08:56:13 bare-galaxy galaxyctl[6286]: galaxy.tools.search DEBUG 2023-11-27 08:56:13,447 [pN:main.1,p:62>
Nov 27 08:56:13 bare-galaxy galaxyctl[6286]: galaxy.tools.search DEBUG 2023-11-27 08:56:13,449 [pN:main.1,p:62>
Nov 27 08:56:13 bare-galaxy galaxyctl[6286]: galaxy.tools.search DEBUG 2023-11-27 08:56:13,756 [pN:main.1,p:62>
Nov 27 08:56:13 bare-galaxy galaxyctl[6286]: galaxy.queue_worker INFO 2023-11-27 08:56:13,767 [pN:main.1,p:628>
Nov 27 08:56:13 bare-galaxy galaxyctl[6286]: galaxy.tools.search DEBUG 2023-11-27 08:56:13,767 [pN:main.1,p:62>
Nov 27 08:56:13 bare-galaxy galaxyctl[6286]: galaxy.tools.search DEBUG 2023-11-27 08:56:13,772 [pN:main.1,p:62>
Nov 27 08:56:13 bare-galaxy galaxyctl[6286]: galaxy.tools.search DEBUG 2023-11-27 08:56:13,772 [pN:main.1,p:62>
Nov 27 08:56:13 bare-galaxy galaxyctl[6286]: galaxy.tools.search DEBUG 2023-11-27 08:56:13,776 [pN:main.1,p:62>
Nov 27 08:56:13 bare-galaxy galaxyctl[6286]: galaxy.tools.search DEBUG 2023-11-27 08:56:13,776 [pN:main.1,p:62>
Nov 27 08:56:13 bare-galaxy galaxyctl[6286]: galaxy.tools.search DEBUG 2023-11-27 08:56:13,779 [pN:main.1,p:62>

2 replies

drosofff Nov 27, 2023
Maintainer Author

CoralineBernachot Nov 27, 2023

repository samtool_filter2 installed successfully (in 0:00:20.478489) at revision 649a225999a5
(26/27) Installing repository sambamba from artbio to section "Samtools" at revision de833cc76a8e (TRT: 0:15:48.395218)
        repository sambamba installed successfully (in 0:00:28.391793) at revision de833cc76a8e
(27/27) Installing repository bedtools from iuc to section "Bedtools" at revision a1a923cd89e8 (TRT: 0:16:16.787236)
        repository bedtools installed successfully (in 0:00:50.794091) at revision a1a923cd89e8
Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:17:07.581794

AstridCanal · 2023-11-27T09:31:31Z

AstridCanal
Nov 27, 2023

● galaxy-gunicorn.service - Galaxy gunicorn
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)
     Active: active (running) since Mon 2023-11-27 08:57:14 UTC; 59s ago
   Main PID: 6094 (gunicorn)
      Tasks: 14 (limit: 38496)
     Memory: 463.7M
        CPU: 21.011s
     CGroup: /system.slice/galaxy-gunicorn.service
             ├─6094 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_f>
             └─6162 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_f>

Nov 27 08:57:38 bare-galaxy galaxyctl[6162]: galaxy.tools.search DEBUG 2023-11-27 08:57:38,990 [pN:main.1,p:61>
Nov 27 08:57:38 bare-galaxy galaxyctl[6162]: galaxy.tools.search DEBUG 2023-11-27 08:57:38,991 [pN:main.1,p:61>
Nov 27 08:57:39 bare-galaxy galaxyctl[6162]: galaxy.tools.search DEBUG 2023-11-27 08:57:39,478 [pN:main.1,p:61>
Nov 27 08:57:39 bare-galaxy galaxyctl[6162]: galaxy.queue_worker INFO 2023-11-27 08:57:39,489 [pN:main.1,p:616>
Nov 27 08:57:39 bare-galaxy galaxyctl[6162]: galaxy.tools.search DEBUG 2023-11-27 08:57:39,489 [pN:main.1,p:61>
Nov 27 08:57:39 bare-galaxy galaxyctl[6162]: galaxy.tools.search DEBUG 2023-11-27 08:57:39,496 [pN:main.1,p:61>
Nov 27 08:57:39 bare-galaxy galaxyctl[6162]: galaxy.tools.search DEBUG 2023-11-27 08:57:39,496 [pN:main.1,p:61>
Nov 27 08:57:39 bare-galaxy galaxyctl[6162]: galaxy.tools.search DEBUG 2023-11-27 08:57:39,502 [pN:main.1,p:61>
Nov 27 08:57:39 bare-galaxy galaxyctl[6162]: galaxy.tools.search DEBUG 2023-11-27 08:57:39,503 [pN:main.1,p:61>
Nov 27 08:57:39 bare-galaxy galaxyctl[6162]: galaxy.tools.search DEBUG 2023-11-27 08:57:39,508 [pN:main.1,p:61>

● galaxy-celery.service - Galaxy celery
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)
     Active: active (running) since Mon 2023-11-27 08:57:14 UTC; 59s ago
   Main PID: 6089 (celery)
      Tasks: 2 (limit: 38496)
     Memory: 192.6M
        CPU: 7.171s
     CGroup: /system.slice/galaxy-celery.service
             ├─6089 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker --c>
             └─6151 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main(7)

Nov 27 08:57:21 bare-galaxy galaxyctl[6089]: [2023-11-27 08:57:21,990: INFO/MainProcess] Connected to sqlalche>
Nov 27 08:57:21 bare-galaxy galaxyctl[6089]: [2023-11-27 08:57:21,990: DEBUG/MainProcess] ^-- substep ok
lines 1-35

Il me manque beat..

3 replies

AstridCanal Nov 27, 2023

repository samtool_filter2 installed successfully (in 0:00:33.522092) at revision 649a225999a5
(26/27) Installing repository sambamba from artbio to section "Samtools" at revision de833cc76a8e (TRT: 0:26:37.484899)
        repository sambamba installed successfully (in 0:00:46.311581) at revision de833cc76a8e
(27/27) Installing repository bedtools from iuc to section "Bedtools" at revision a1a923cd89e8 (TRT: 0:27:23.796847)
        repository bedtools installed successfully (in 0:01:27.091824) at revision a1a923cd89e8
Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:28:50.889783

drosofff Nov 27, 2023
Maintainer Author

Il me manque beat..

Ca ça dépend de la commande que vous avez utilisée... et que vous n'avez pas copiée ;-)

AstridCanal Nov 27, 2023

root@bare-galaxy:~# systemctl status galaxy*.service

yeloett · 2023-11-27T10:16:51Z

yeloett
Nov 27, 2023

root@bare-galaxy:~# systemctl status galaxy*.service                                                           
● galaxy-celery.service - Galaxy celery                                                                        
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)              
     Active: active (running) since Mon 2023-11-27 09:49:41 UTC; 8min ago                                      
   Main PID: 5579 (celery)                                                                                     
      Tasks: 2 (limit: 38496)                                                                                  
     Memory: 192.3M                                                                                            
        CPU: 11.711s                                                                                           
     CGroup: /system.slice/galaxy-celery.service                                                               
             ├─5579 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker --c>
             └─5616 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main(7)

Nov 27 09:49:48 bare-galaxy galaxyctl[5579]: [2023-11-27 09:49:48,423: INFO/MainProcess] Connected to sqlalche>
Nov 27 09:49:48 bare-galaxy galaxyctl[5579]: [2023-11-27 09:49:48,424: DEBUG/MainProcess] ^-- substep ok
Nov 27 09:49:48 bare-galaxy galaxyctl[5579]: [2023-11-27 09:49:48,424: DEBUG/MainProcess] | Consumer: Starting>
Nov 27 09:49:48 bare-galaxy galaxyctl[5579]: [2023-11-27 09:49:48,424: DEBUG/MainProcess] ^-- substep ok
Nov 27 09:49:48 bare-galaxy galaxyctl[5579]: [2023-11-27 09:49:48,424: DEBUG/MainProcess] | Consumer: Starting>
Nov 27 09:49:48 bare-galaxy galaxyctl[5579]: [2023-11-27 09:49:48,530: DEBUG/MainProcess] ^-- substep ok
Nov 27 09:49:48 bare-galaxy galaxyctl[5579]: [2023-11-27 09:49:48,531: DEBUG/MainProcess] | Consumer: Starting>
Nov 27 09:49:48 bare-galaxy galaxyctl[5579]: [2023-11-27 09:49:48,531: DEBUG/MainProcess] ^-- substep ok
Nov 27 09:49:48 bare-galaxy galaxyctl[5579]: [2023-11-27 09:49:48,531: DEBUG/MainProcess] | Consumer: Starting>
Nov 27 09:49:48 bare-galaxy galaxyctl[5579]: [2023-11-27 09:49:48,531: INFO/MainProcess] celery@bare-galaxy re>

● galaxy-gunicorn.service - Galaxy gunicorn
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)
     Active: active (running) since Mon 2023-11-27 09:49:41 UTC; 8min ago
   Main PID: 5580 (gunicorn)
      Tasks: 14 (limit: 38496)
     Memory: 463.1M
        CPU: 47.448s
     CGroup: /system.slice/galaxy-gunicorn.service
             ├─5580 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_f>
             └─5617 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_f>

Nov 27 09:50:05 bare-galaxy galaxyctl[5617]: galaxy.tools.search DEBUG 2023-11-27 09:50:05,588 [pN:main.1,p:56>
Nov 27 09:50:05 bare-galaxy galaxyctl[5617]: galaxy.tools.search DEBUG 2023-11-27 09:50:05,590 [pN:main.1,p:56>
Nov 27 09:50:06 bare-galaxy galaxyctl[5617]: galaxy.tools.search DEBUG 2023-11-27 09:50:06,072 [pN:main.1,p:56>
Nov 27 09:50:06 bare-galaxy galaxyctl[5617]: galaxy.queue_worker INFO 2023-11-27 09:50:06,119 [pN:main.1,p:561>
Nov 27 09:50:06 bare-galaxy galaxyctl[5617]: galaxy.tools.search DEBUG 2023-11-27 09:50:06,119 [pN:main.1,p:56>
Nov 27 09:50:06 bare-galaxy galaxyctl[5617]: galaxy.tools.search DEBUG 2023-11-27 09:50:06,126 [pN:main.1,p:56>
Nov 27 09:50:06 bare-galaxy galaxyctl[5617]: galaxy.tools.search DEBUG 2023-11-27 09:50:06,126 [pN:main.1,p:56>
Nov 27 09:50:06 bare-galaxy galaxyctl[5617]: galaxy.tools.search DEBUG 2023-11-27 09:50:06,131 [pN:main.1,p:56>
Nov 27 09:50:06 bare-galaxy galaxyctl[5617]: galaxy.tools.search DEBUG 2023-11-27 09:50:06,131 [pN:main.1,p:56>
Nov 27 09:50:06 bare-galaxy galaxyctl[5617]: galaxy.tools.search DEBUG 2023-11-27 09:50:06,136 [pN:main.1,p:56>

● galaxy-celery-beat.service - Galaxy celery-beat
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)
     Active: active (running) since Mon 2023-11-27 09:49:41 UTC; 8min ago
   Main PID: 5578 (celery)
      Tasks: 1 (limit: 38496)
     Memory: 188.0M
        CPU: 6.079s
     CGroup: /system.slice/galaxy-celery-beat.service
             └─5578 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat --log>

Nov 27 09:49:48 bare-galaxy galaxyctl[5578]: [2023-11-27 09:49:48,357: DEBUG/MainProcess] Current schedule:
Nov 27 09:49:48 bare-galaxy galaxyctl[5578]: <ScheduleEntry: cleanup-short-term-storage galaxy.cleanup_short_t>
Nov 27 09:49:48 bare-galaxy galaxyctl[5578]: <ScheduleEntry: prune-history-audit-table galaxy.prune_history_au>
Nov 27 09:49:48 bare-galaxy galaxyctl[5578]: <ScheduleEntry: clean-object-store-caches galaxy.clean_object_sto>
Nov 27 09:49:48 bare-galaxy galaxyctl[5578]: <ScheduleEntry: cleanup-expired-notifications galaxy.cleanup_expi>
Nov 27 09:49:48 bare-galaxy galaxyctl[5578]: <ScheduleEntry: celery.backend_cleanup celery.backend_cleanup() <>
Nov 27 09:49:48 bare-galaxy galaxyctl[5578]: [2023-11-27 09:49:48,357: DEBUG/MainProcess] beat: Ticking with m>
Nov 27 09:49:48 bare-galaxy galaxyctl[5578]: [2023-11-27 09:49:48,359: DEBUG/MainProcess] beat: Waking up in 5>
Nov 27 09:54:48 bare-galaxy galaxyctl[5578]: [2023-11-27 09:54:48,460: DEBUG/MainProcess] beat: Synchronizing >
Nov 27 09:54:48 bare-galaxy galaxyctl[5578]: [2023-11-27 09:54:48,462: DEBUG/MainProcess] beat: Waking up in 5>

1 reply

yeloett Nov 27, 2023

(.venv) root@bare-galaxy:~# tail -f tools.log
        repository samtool_filter2 installed successfully (in 0:00:30.587706) at revision 649a225999a5
(26/27) Installing repository sambamba from artbio to section "Samtools" at revision de833cc76a8e (TRT: 0:25:17.097613)
        repository sambamba installed successfully (in 0:00:42.045801) at revision de833cc76a8e
(27/27) Installing repository bedtools from iuc to section "Bedtools" at revision a1a923cd89e8 (TRT: 0:25:59.143670)
        repository bedtools installed successfully (in 0:01:23.445774) at revision a1a923cd89e8
Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:27:22.590079

AlixMartin1 · 2023-11-27T17:21:01Z

AlixMartin1
Nov 27, 2023

● galaxy-celery-beat.service - Galaxy celery-beat                                                                                                                          
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)                                                                    
     Active: active (running) since Mon 2023-11-27 17:10:29 UTC; 2min 3s ago                                                                                              
   Main PID: 5534 (celery)                                                                                                                                                
      Tasks: 1 (limit: 38496)                                                                                                                                              
     Memory: 186.3M                                                                                                                                                        
        CPU: 5.991s  
     CGroup: /system.slice/galaxy-celery-beat.service
             └─5534 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat --loglevel DEBUG --schedule /root/galaxy/database/gravity/celery-beat-schedule

Nov 27 17:10:35 bare-galaxy galaxyctl[5534]: [2023-11-27 17:10:35,505: DEBUG/MainProcess] Setting default socket timeout to 30
Nov 27 17:10:35 bare-galaxy galaxyctl[5534]: [2023-11-27 17:10:35,506: INFO/MainProcess] beat: Starting...
Nov 27 17:10:35 bare-galaxy galaxyctl[5534]: [2023-11-27 17:10:35,542: DEBUG/MainProcess] Current schedule:
Nov 27 17:10:35 bare-galaxy galaxyctl[5534]: <ScheduleEntry: cleanup-short-term-storage galaxy.cleanup_short_term_storage() <freq: 1.00 hour>
Nov 27 17:10:35 bare-galaxy galaxyctl[5534]: <ScheduleEntry: prune-history-audit-table galaxy.prune_history_audit_table() <freq: 1.00 hour>
Nov 27 17:10:35 bare-galaxy galaxyctl[5534]: <ScheduleEntry: clean-object-store-caches galaxy.clean_object_store_caches() <freq: 10.00 minutes>
Nov 27 17:10:35 bare-galaxy galaxyctl[5534]: <ScheduleEntry: cleanup-expired-notifications galaxy.cleanup_expired_notifications() <freq: 1.00 day>
Nov 27 17:10:35 bare-galaxy galaxyctl[5534]: <ScheduleEntry: celery.backend_cleanup celery.backend_cleanup() <crontab: 0 4 * * * (m/h/d/dM/MY)>
Nov 27 17:10:35 bare-galaxy galaxyctl[5534]: [2023-11-27 17:10:35,542: DEBUG/MainProcess] beat: Ticking with max interval->5.00 minutes
Nov 27 17:10:35 bare-galaxy galaxyctl[5534]: [2023-11-27 17:10:35,544: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.

● galaxy-gunicorn.service - Galaxy gunicorn
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)
     Active: active (running) since Mon 2023-11-27 17:10:29 UTC; 2min 3s ago
   Main PID: 5536 (gunicorn)
      Tasks: 14 (limit: 38496)
     Memory: 462.9M
        CPU: 24.405s
     CGroup: /system.slice/galaxy-gunicorn.service
             ├─5536 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b [0.0.0.0:80](http://0.0.0.0/) --workers=1 --confi>
             └─5573 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b [0.0.0.0:80](http://0.0.0.0/) --workers=1 --confi>

Nov 27 17:10:52 bare-galaxy galaxyctl[5573]: galaxy.tools.search DEBUG 2023-11-27 17:10:52,361 [pN:main.1,p:5573,tN:Thread-1] Toolbox index of panel ontology:edam_operations finished (437.672 ms)
Nov 27 17:10:52 bare-galaxy galaxyctl[5573]: galaxy.tools.search DEBUG 2023-11-27 17:10:52,363 [pN:main.1,p:5573,tN:Thread-1] Starting to build toolbox index of panel ontology:edam_topics.
Nov 27 17:10:52 bare-galaxy galaxyctl[5573]: galaxy.tools.search DEBUG 2023-11-27 17:10:52,845 [pN:main.1,p:5573,tN:Thread-1] Toolbox index of panel ontology:edam_topics finished (481.621 ms)
Nov 27 17:10:52 bare-galaxy galaxyctl[5573]: galaxy.queue_worker INFO 2023-11-27 17:10:52,875 [pN:main.1,p:5573,tN:Thread-1] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
Nov 27 17:10:52 bare-galaxy galaxyctl[5573]: galaxy.tools.search DEBUG 2023-11-27 17:10:52,876 [pN:main.1,p:5573,tN:Thread-1] Starting to build toolbox index of panel default.
Nov 27 17:10:52 bare-galaxy galaxyctl[5573]: galaxy.tools.search DEBUG 2023-11-27 17:10:52,882 [pN:main.1,p:5573,tN:Thread-1] Toolbox index of panel default finished (6.119 ms)
Nov 27 17:10:52 bare-galaxy galaxyctl[5573]: galaxy.tools.search DEBUG 2023-11-27 17:10:52,883 [pN:main.1,p:5573,tN:Thread-1] Starting to build toolbox index of panel ontology:edam_operations.
Nov 27 17:10:52 bare-galaxy galaxyctl[5573]: galaxy.tools.search DEBUG 2023-11-27 17:10:52,888 [pN:main.1,p:5573,tN:Thread-1] Toolbox index of panel ontology:edam_operations finished (4.861 ms)
Nov 27 17:10:52 bare-galaxy galaxyctl[5573]: galaxy.tools.search DEBUG 2023-11-27 17:10:52,888 [pN:main.1,p:5573,tN:Thread-1] Starting to build toolbox index of panel ontology:edam_topics.
Nov 27 17:10:52 bare-galaxy galaxyctl[5573]: galaxy.tools.search DEBUG 2023-11-27 17:10:52,893 [pN:main.1,p:5573,tN:Thread-1] Toolbox index of panel ontology:edam_topics finished (4.320 ms)

● galaxy-celery.service - Galaxy celery
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)
     Active: active (running) since Mon 2023-11-27 17:10:29 UTC; 2min 3s ago
   Main PID: 5535 (celery)
      Tasks: 2 (limit: 38496)
     Memory: 194.7M
        CPU: 7.509s
     CGroup: /system.slice/galaxy-celery.service
             ├─5535 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker --concurrency 2 --loglevel DEBUG --pool threads --queues celery,galaxy.internal,galaxy.external
             └─5572 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main(7)

Nov 27 17:10:35 bare-galaxy galaxyctl[5535]: [2023-11-27 17:10:35,609: INFO/MainProcess] Connected to sqlalchemy+sqlite:////root/galaxy/database/control.sqlite
Nov 27 17:10:35 bare-galaxy galaxyctl[5535]: [2023-11-27 17:10:35,609: DEBUG/MainProcess] ^-- substep ok
Nov 27 17:10:35 bare-galaxy galaxyctl[5535]: [2023-11-27 17:10:35,609: DEBUG/MainProcess] | Consumer: Starting Events
Nov 27 17:10:35 bare-galaxy galaxyctl[5535]: [2023-11-27 17:10:35,610: DEBUG/MainProcess] ^-- substep ok
Nov 27 17:10:35 bare-galaxy galaxyctl[5535]: [2023-11-27 17:10:35,610: DEBUG/MainProcess] | Consumer: Starting Heart
Nov 27 17:10:35 bare-galaxy galaxyctl[5535]: [2023-11-27 17:10:35,610: DEBUG/MainProcess] ^-- substep ok
Nov 27 17:10:35 bare-galaxy galaxyctl[5535]: [2023-11-27 17:10:35,610: DEBUG/MainProcess] | Consumer: Starting Tasks
Nov 27 17:10:36 bare-galaxy galaxyctl[5535]: [2023-11-27 17:10:36,043: DEBUG/MainProcess] ^-- substep ok
Nov 27 17:10:36 bare-galaxy galaxyctl[5535]: [2023-11-27 17:10:36,043: DEBUG/MainProcess] | Consumer: Starting event loop
Nov 27 17:10:36 bare-galaxy galaxyctl[5535]: [2023-11-27 17:10:36,044: INFO/MainProcess] celery@bare-galaxy ready.

1 reply

AlixMartin1 Nov 27, 2023

repository samtool_filter2 installed successfully (in 0:00:30.592653) at revision 649a225999a5
(26/27) Installing repository sambamba from artbio to section "Samtools" at revision de833cc76a8e (TRT: 0:25:33.899815)
        repository sambamba installed successfully (in 0:00:40.749516) at revision de833cc76a8e
(27/27) Installing repository bedtools from iuc to section "Bedtools" at revision a1a923cd89e8 (TRT: 0:26:14.649583)
        repository bedtools installed successfully (in 0:01:21.934624) at revision a1a923cd89e8
Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:27:36.584707

laureasselin · 2023-11-27T20:13:49Z

laureasselin
Nov 27, 2023

systemctl status galaxy*.service                                                                                                                                
● galaxy-celery-beat.service - Galaxy celery-beat                                                                                                                                   
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)                                                                              
     Active: active (running) since Mon 2023-11-27 19:52:10 UTC; 24s ago                                                                                                            
   Main PID: 6374 (celery)                                                                                                                                                          
      Tasks: 1 (limit: 38496)                                                                                                                                                       
     Memory: 188.0M                                                                                                                                                                 
        CPU: 13.321s                                                                                                                                                                
     CGroup: /system.slice/galaxy-celery-beat.service                                                                                                                               



et: enabled)






xy.celery beat --loglevel DEBUG --schedule /root/galaxy/database/gravity/celery-beat-schedule

Setting default socket timeout to 30
eat: Starting...
Current schedule:
axy.clean_object_store_caches() <freq: 10.00 minutes>
 galaxy.cleanup_expired_notifications() <freq: 1.00 day>
axy.prune_history_audit_table() <freq: 1.00 hour>
laxy.cleanup_short_term_storage() <freq: 1.00 hour>
.backend_cleanup() <crontab: 0 4 * * * (m/h/d/dM/MY)>
beat: Ticking with max interval->5.00 minutes
beat: Waking up in 5.00 minutes.


 enabled)






ebapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b 0.0.0.0:80 --workers=1 --config python:galaxy.web_stack.gunicorn_con>

7 19:52:33,654 [pN:main,p:6376,tN:MainThread] Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.4 into tool panel..
7 19:52:33,654 [pN:main,p:6376,tN:MainThread] Loaded tool id: gene2exon1, version: 1.0.0 into tool panel..
7 19:52:33,654 [pN:main,p:6376,tN:MainThread] Loaded tool id: Count1, version: 1.0.3 into tool panel..
7 19:52:33,654 [pN:main,p:6376,tN:MainThread] Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.1 into tool panel..
7 19:52:33,654 [pN:main,p:6376,tN:MainThread] Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel..
7 19:52:33,654 [pN:main,p:6376,tN:MainThread] Loaded tool id: hgv_david, version: 1.0.1 into tool panel..
7 19:52:33,654 [pN:main,p:6376,tN:MainThread] Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel..
7 19:52:33,654 [pN:main,p:6376,tN:MainThread] Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel..
3-11-27 19:52:33,654 [pN:main,p:6376,tN:MainThread] Loading EDAM tool panel finished (9.822 ms)
UG 2023-11-27 19:52:33,655 [pN:main,p:6376,tN:MainThread] Writing integrated tool panel config file to '/root/galaxy/config/integrated_tool_panel.xml'


nabled)






xy.celery worker --concurrency 2 --loglevel DEBUG --pool threads --queues celery,galaxy.internal,galaxy.external
 import main;main(7)

onnected to sqlalchemy+sqlite:////root/galaxy/database/control.sqlite
^-- substep ok
| Consumer: Starting Events
^-- substep ok
| Consumer: Starting Tasks
^-- substep ok
| Consumer: Starting Heart
^-- substep ok
| Consumer: Starting event loop
elery@bare-galaxy ready

1 reply

drosofff Nov 27, 2023
Maintainer Author

Vous avez réussi un copier/coller étrange... Je voudrais le faire, je n'y arriverais pas je crois ;-)

laureasselin · 2023-11-27T20:57:32Z

laureasselin
Nov 27, 2023

 root@bare-galaxy:~#  tail -f tools.log 
        repository samtool_filter2 installed successfully (in 0:00:31.826933) at revision 649a225999a5
(26/27) Installing repository sambamba from artbio to section "Samtools" at revision de833cc76a8e (TRT: 0:25:23.103938)
        repository sambamba installed successfully (in 0:00:41.774158) at revision de833cc76a8e
(27/27) Installing repository bedtools from iuc to section "Bedtools" at revision a1a923cd89e8 (TRT: 0:26:04.878391)
        repository bedtools installed successfully (in 0:01:22.468929) at revision a1a923cd89e8
Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:27:27.347848

0 replies

MarieMassier · 2023-11-28T18:08:58Z

MarieMassier
Nov 28, 2023

galaxy-gunicorn.service - Galaxy gunicorn                                                                    
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)            
     Active: active (running) since Tue 2023-11-28 17:53:21 UTC; 12min ago                                     
   Main PID: 6291 (gunicorn)      Tasks: 14 (limit: 38496)       
     Memory: 465.6M                                                                                            
        CPU: 56.394s                                                                                           
     CGroup: /system.slice/galaxy-gunicorn.service                                                             
             ├─6291 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() -->
             └─6328 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() -->

Nov 28 17:53:44 bare-galaxy galaxyctl[6328]: galaxy.tools.search DEBUG 2023-11-28 17:53:44,186 [pN:main.1,p:6328,tN:Thread-1] Too>
Nov 28 17:53:44 bare-galaxy galaxyctl[6328]: galaxy.tools.search DEBUG 2023-11-28 17:53:44,188 [pN:main.1,p:6328,tN:Thread-1] Sta>
Nov 28 17:53:44 bare-galaxy galaxyctl[6328]: galaxy.tools.search DEBUG 2023-11-28 17:53:44,646 [pN:main.1,p:6328,tN:Thread-1] Too>
Nov 28 17:53:44 bare-galaxy galaxyctl[6328]: galaxy.queue_worker INFO 2023-11-28 17:53:44,656 [pN:main.1,p:6328,tN:Thread-1] Inst>
Nov 28 17:53:44 bare-galaxy galaxyctl[6328]: galaxy.tools.search DEBUG 2023-11-28 17:53:44,656 [pN:main.1,p:6328,tN:Thread-1] Sta>
Nov 28 17:53:44 bare-galaxy galaxyctl[6328]: galaxy.tools.search DEBUG 2023-11-28 17:53:44,661 [pN:main.1,p:6328,tN:Thread-1] Too>
Nov 28 17:53:44 bare-galaxy galaxyctl[6328]: galaxy.tools.search DEBUG 2023-11-28 17:53:44,662 [pN:main.1,p:6328,tN:Thread-1] Sta>
Nov 28 17:53:44 bare-galaxy galaxyctl[6328]: galaxy.tools.search DEBUG 2023-11-28 17:53:44,666 [pN:main.1,p:6328,tN:Thread-1] Too>
Nov 28 17:53:44 bare-galaxy galaxyctl[6328]: galaxy.tools.search DEBUG 2023-11-28 17:53:44,666 [pN:main.1,p:6328,tN:Thread-1] Sta>
Nov 28 17:53:44 bare-galaxy galaxyctl[6328]: galaxy.tools.search DEBUG 2023-11-28 17:53:44,670 [pN:main.1,p:6328,tN:Thread-1] Too>

● galaxy-celery-beat.service - Galaxy celery-beat
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)
     Active: active (running) since Tue 2023-11-28 17:53:21 UTC; 12min ago
   Main PID: 6289 (celery)
      Tasks: 1 (limit: 38496)
     Memory: 186.5M
        CPU: 5.628s
     CGroup: /system.slice/galaxy-celery-beat.service
             └─6289 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat --loglevel DEBUG --sched>

Nov 28 17:53:27 bare-galaxy galaxyctl[6289]: <ScheduleEntry: prune-history-audit-table galaxy.prune_history_audit_table() <freq: >
Nov 28 17:53:27 bare-galaxy galaxyctl[6289]: <ScheduleEntry: celery.backend_cleanup celery.backend_cleanup() <crontab: 0 4 * * * >
Nov 28 17:53:27 bare-galaxy galaxyctl[6289]: [2023-11-28 17:53:27,421: DEBUG/MainProcess] beat: Ticking with max interval->5.00 m>
Nov 28 17:53:27 bare-galaxy galaxyctl[6289]: [2023-11-28 17:53:27,422: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.
Nov 28 17:58:27 bare-galaxy galaxyctl[6289]: [2023-11-28 17:58:27,522: DEBUG/MainProcess] beat: Synchronizing schedule...
Nov 28 17:58:27 bare-galaxy galaxyctl[6289]: [2023-11-28 17:58:27,525: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.
Nov 28 18:03:27 bare-galaxy galaxyctl[6289]: [2023-11-28 18:03:27,491: DEBUG/MainProcess] beat: Synchronizing schedule...
Nov 28 18:03:27 bare-galaxy galaxyctl[6289]: [2023-11-28 18:03:27,501: INFO/MainProcess] Scheduler: Sending due task clean-object>
Nov 28 18:03:27 bare-galaxy galaxyctl[6289]: [2023-11-28 18:03:27,533: DEBUG/MainProcess] galaxy.clean_object_store_caches sent. >
Nov 28 18:03:27 bare-galaxy galaxyctl[6289]: [2023-11-28 18:03:27,534: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.

● galaxy-celery.service - Galaxy celery
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)
     Active: active (running) since Tue 2023-11-28 17:53:21 UTC; 12min ago
   Main PID: 6290 (celery)
      Tasks: 3 (limit: 38496)
     Memory: 230.0M
        CPU: 14.173s
     CGroup: /system.slice/galaxy-celery.service
             ├─6290 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker --concurrency 2 --logl>
             └─6327 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main(7)

Nov 28 18:03:29 bare-galaxy galaxyctl[6290]: [2023-11-28 18:03:29,402: DEBUG/main] Loaded build site 'ensembl': tool-data/shared/>
Nov 28 18:03:29 bare-galaxy galaxyctl[6290]: [2023-11-28 18:03:29,402: DEBUG/main] Loaded build site 'ensembl_data_url': tool-dat>
Nov 28 18:03:29 bare-galaxy galaxyctl[6290]: [2023-11-28 18:03:29,402: DEBUG/main] Build site file [tool-data/shared/igv/igv_buil>
Nov 28 18:03:29 bare-galaxy galaxyctl[6290]: [2023-11-28 18:03:29,402: DEBUG/main] Loaded build site 'igv': tool-data/shared/igv/>
Nov 28 18:03:29 bare-galaxy galaxyctl[6290]: [2023-11-28 18:03:29,402: DEBUG/main] Build site file [tool-data/shared/rviewer/rvie>
Nov 28 18:03:29 bare-galaxy galaxyctl[6290]: [2023-11-28 18:03:29,402: DEBUG/main] Loaded build site 'rviewer': tool-data/shared/>
Nov 28 18:03:29 bare-galaxy galaxyctl[6290]: [2023-11-28 18:03:29,407: DEBUG/main] Loading references to tool sheds from internal>
Nov 28 18:03:29 bare-galaxy galaxyctl[6290]: [2023-11-28 18:03:29,407: DEBUG/main] Loaded reference to tool shed: Galaxy Main Too>
Nov 28 18:03:29 bare-galaxy galaxyctl[6290]: [2023-11-28 18:03:29,408: INFO/main] Successfully executed Celery task clean_object_>
Nov 28 18:03:29 bare-galaxy galaxyctl[6290]: [2023-11-28 18:03:29,417: INFO/main] Task galaxy.clean_object_store_caches[1faf8025->
lines 30-64/64 (END)

0 replies

MarieMassier · 2023-11-28T18:48:00Z

MarieMassier
Nov 28, 2023

(.venv) root@bare-galaxy:~# tail -f tools.log 
        repository samtool_filter2 installed successfully (in 0:00:31.615161) at revision 649a225999a5
(26/27) Installing repository sambamba from artbio to section "Samtools" at revision de833cc76a8e (TRT: 0:25:15.398050)
        repository sambamba installed successfully (in 0:00:39.819674) at revision de833cc76a8e
(27/27) Installing repository bedtools from iuc to section "Bedtools" at revision a1a923cd89e8 (TRT: 0:25:55.217947)
        repository bedtools installed successfully (in 0:01:21.877344) at revision a1a923cd89e8
Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:27:17.095844

0 replies

SabineVautier · 2023-11-29T19:34:31Z

SabineVautier
Nov 29, 2023

  galaxy-gunicorn.service - Galaxy gunicorn
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)
     Active: active (running) since Wed 2023-11-29 19:26:19 UTC; 3min 52s ago
   Main PID: 17868 (gunicorn)
      Tasks: 14 (limit: 38496)
     Memory: 462.1M
        CPU: 44.952s
     CGroup: /system.slice/galaxy-gunicorn.service
             ├─17868 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib -k gal>
             └─17938 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib -k gal>

Nov 29 19:26:57 bare-galaxy galaxyctl[17938]: galaxy.tools.search DEBUG 2023-11-29 19:26:57,172 [pN:main.1,p:17938,tN:Thread-1] Toolbox index of panel ontology:edam_>
Nov 29 19:26:57 bare-galaxy galaxyctl[17938]: galaxy.tools.search DEBUG 2023-11-29 19:26:57,175 [pN:main.1,p:17938,tN:Thread-1] Starting to build toolbox index of pa>
Nov 29 19:26:58 bare-galaxy galaxyctl[17938]: galaxy.tools.search DEBUG 2023-11-29 19:26:58,194 [pN:main.1,p:17938,tN:Thread-1] Toolbox index of panel ontology:edam_>
Nov 29 19:26:58 bare-galaxy galaxyctl[17938]: galaxy.queue_worker INFO 2023-11-29 19:26:58,213 [pN:main.1,p:17938,tN:Thread-1] Instance 'main.1' received 'rebuild_to>
Nov 29 19:26:58 bare-galaxy galaxyctl[17938]: galaxy.tools.search DEBUG 2023-11-29 19:26:58,214 [pN:main.1,p:17938,tN:Thread-1] Starting to build toolbox index of pa>
Nov 29 19:26:58 bare-galaxy galaxyctl[17938]: galaxy.tools.search DEBUG 2023-11-29 19:26:58,227 [pN:main.1,p:17938,tN:Thread-1] Toolbox index of panel default finish>
Nov 29 19:26:58 bare-galaxy galaxyctl[17938]: galaxy.tools.search DEBUG 2023-11-29 19:26:58,228 [pN:main.1,p:17938,tN:Thread-1] Starting to build toolbox index of pa>
Nov 29 19:26:58 bare-galaxy galaxyctl[17938]: galaxy.tools.search DEBUG 2023-11-29 19:26:58,238 [pN:main.1,p:17938,tN:Thread-1] Toolbox index of panel ontology:edam_>
Nov 29 19:26:58 bare-galaxy galaxyctl[17938]: galaxy.tools.search DEBUG 2023-11-29 19:26:58,238 [pN:main.1,p:17938,tN:Thread-1] Starting to build toolbox index of pa>
Nov 29 19:26:58 bare-galaxy galaxyctl[17938]: galaxy.tools.search DEBUG 2023-11-29 19:26:58,249 [pN:main.1,p:17938,tN:Thread-1] Toolbox index of panel ontology:edam_>

● galaxy-celery-beat.service - Galaxy celery-beat
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)
     Active: active (running) since Wed 2023-11-29 19:26:19 UTC; 3min 52s ago
   Main PID: 17862 (celery)
      Tasks: 1 (limit: 38496)
     Memory: 185.2M
        CPU: 8.031s
     CGroup: /system.slice/galaxy-celery-beat.service
             └─17862 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat --loglevel DEBUG --schedule /root/galaxy/database/gravity/c>

Nov 29 19:26:27 bare-galaxy galaxyctl[17862]: [2023-11-29 19:26:27,534: DEBUG/MainProcess] Setting default socket timeout to 30
Nov 29 19:26:27 bare-galaxy galaxyctl[17862]: [2023-11-29 19:26:27,535: INFO/MainProcess] beat: Starting...
Nov 29 19:26:27 bare-galaxy galaxyctl[17862]: [2023-11-29 19:26:27,634: DEBUG/MainProcess] Current schedule:
Nov 29 19:26:27 bare-galaxy galaxyctl[17862]: <ScheduleEntry: prune-history-audit-table galaxy.prune_history_audit_table() <freq: 1.00 hour>
Nov 29 19:26:27 bare-galaxy galaxyctl[17862]: <ScheduleEntry: clean-object-store-caches galaxy.clean_object_store_caches() <freq: 10.00 minutes>
Nov 29 19:26:27 bare-galaxy galaxyctl[17862]: <ScheduleEntry: cleanup-short-term-storage galaxy.cleanup_short_term_storage() <freq: 1.00 hour>
Nov 29 19:26:27 bare-galaxy galaxyctl[17862]: <ScheduleEntry: cleanup-expired-notifications galaxy.cleanup_expired_notifications() <freq: 1.00 day>
Nov 29 19:26:27 bare-galaxy galaxyctl[17862]: <ScheduleEntry: celery.backend_cleanup celery.backend_cleanup() <crontab: 0 4 * * * (m/h/d/dM/MY)>
Nov 29 19:26:27 bare-galaxy galaxyctl[17862]: [2023-11-29 19:26:27,634: DEBUG/MainProcess] beat: Ticking with max interval->5.00 minutes
Nov 29 19:26:27 bare-galaxy galaxyctl[17862]: [2023-11-29 19:26:27,636: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.

● galaxy-celery.service - Galaxy celery
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)
     Active: active (running) since Wed 2023-11-29 19:26:19 UTC; 3min 52s ago
   Main PID: 17867 (celery)
      Tasks: 2 (limit: 38496)
     Memory: 193.1M
        CPU: 11.259s
     CGroup: /system.slice/galaxy-celery.service
             ├─17867 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker --concurrency 2 --loglevel DEBUG --pool threads --queues >
             └─17937 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main(7)

Nov 29 19:26:27 bare-galaxy galaxyctl[17867]: [2023-11-29 19:26:27,729: INFO/MainProcess] Connected to sqlalchemy+sqlite:////root/galaxy/database/control.sqlite
Nov 29 19:26:27 bare-galaxy galaxyctl[17867]: [2023-11-29 19:26:27,730: DEBUG/MainProcess] ^-- substep ok
Nov 29 19:26:27 bare-galaxy galaxyctl[17867]: [2023-11-29 19:26:27,730: DEBUG/MainProcess] | Consumer: Starting Events
Nov 29 19:26:27 bare-galaxy galaxyctl[17867]: [2023-11-29 19:26:27,731: DEBUG/MainProcess] ^-- substep ok
Nov 29 19:26:27 bare-galaxy galaxyctl[17867]: [2023-11-29 19:26:27,732: DEBUG/MainProcess] | Consumer: Starting Heart
Nov 29 19:26:27 bare-galaxy galaxyctl[17867]: [2023-11-29 19:26:27,732: DEBUG/MainProcess] ^-- substep ok
Nov 29 19:26:27 bare-galaxy galaxyctl[17867]: [2023-11-29 19:26:27,733: DEBUG/MainProcess] | Consumer: Starting Tasks
Nov 29 19:26:27 bare-galaxy galaxyctl[17867]: [2023-11-29 19:26:27,927: DEBUG/MainProcess] ^-- substep ok
Nov 29 19:26:27 bare-galaxy galaxyctl[17867]: [2023-11-29 19:26:27,927: DEBUG/MainProcess] | Consumer: Starting event loop
Nov 29 19:26:27 bare-galaxy galaxyctl[17867]: [2023-11-29 19:26:27,927: INFO/MainProcess] celery@bare-galaxy ready.
lines 26-64/64 (END)

0 replies

Salimaiche · 2023-11-30T11:46:13Z

Salimaiche
Nov 30, 2023

● galaxy-celery-beat.service - Galaxy celery-beat                                                              
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)         
     Active: active (running) since Thu 2023-11-30 11:42:48 UTC; 50s ago                                       
   Main PID: 6304 (celery)                                                                                     
      Tasks: 1 (limit: 38496)                                                                                  
     Memory: 184.4M                                                                                            
        CPU: 6.608s                                                                                            
     CGroup: /system.slice/galaxy-celery-beat.service                                                          
             └─6304 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat --log>
                                                                                                               
Nov 30 11:42:55 bare-galaxy galaxyctl[6304]: [2023-11-30 11:42:55,116: DEBUG/MainProcess] Setting default sock>
Nov 30 11:42:55 bare-galaxy galaxyctl[6304]: [2023-11-30 11:42:55,117: INFO/MainProcess] beat: Starting...
Nov 30 11:42:55 bare-galaxy galaxyctl[6304]: [2023-11-30 11:42:55,165: DEBUG/MainProcess] Current schedule:
Nov 30 11:42:55 bare-galaxy galaxyctl[6304]: <ScheduleEntry: clean-object-store-caches galaxy.clean_object_sto>
Nov 30 11:42:55 bare-galaxy galaxyctl[6304]: <ScheduleEntry: cleanup-short-term-storage galaxy.cleanup_short_t>
Nov 30 11:42:55 bare-galaxy galaxyctl[6304]: <ScheduleEntry: prune-history-audit-table galaxy.prune_history_au>
Nov 30 11:42:55 bare-galaxy galaxyctl[6304]: <ScheduleEntry: cleanup-expired-notifications galaxy.cleanup_expi>
Nov 30 11:42:55 bare-galaxy galaxyctl[6304]: <ScheduleEntry: celery.backend_cleanup celery.backend_cleanup() <>
Nov 30 11:42:55 bare-galaxy galaxyctl[6304]: [2023-11-30 11:42:55,165: DEBUG/MainProcess] beat: Ticking with m>
Nov 30 11:42:55 bare-galaxy galaxyctl[6304]: [2023-11-30 11:42:55,167: DEBUG/MainProcess] beat: Waking up in 5>

● galaxy-gunicorn.service - Galaxy gunicorn
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 11:42:48 UTC; 50s ago
   Main PID: 6306 (gunicorn)
      Tasks: 14 (limit: 38496)
     Memory: 466.8M
        CPU: 23.554s
     CGroup: /system.slice/galaxy-gunicorn.service
             ├─6306 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_f>
             └─6345 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_f>

Nov 30 11:43:15 bare-galaxy galaxyctl[6345]: galaxy.tools.search DEBUG 2023-11-30 11:43:15,667 [pN:main.1,p:63>
Nov 30 11:43:15 bare-galaxy galaxyctl[6345]: galaxy.tools.search DEBUG 2023-11-30 11:43:15,669 [pN:main.1,p:63>
Nov 30 11:43:16 bare-galaxy galaxyctl[6345]: galaxy.tools.search DEBUG 2023-11-30 11:43:16,252 [pN:main.1,p:63>
Nov 30 11:43:16 bare-galaxy galaxyctl[6345]: galaxy.queue_worker INFO 2023-11-30 11:43:16,263 [pN:main.1,p:634>
Nov 30 11:43:16 bare-galaxy galaxyctl[6345]: galaxy.tools.search DEBUG 2023-11-30 11:43:16,263 [pN:main.1,p:63>
Nov 30 11:43:16 bare-galaxy galaxyctl[6345]: galaxy.tools.search DEBUG 2023-11-30 11:43:16,271 [pN:main.1,p:63>
Nov 30 11:43:16 bare-galaxy galaxyctl[6345]: galaxy.tools.search DEBUG 2023-11-30 11:43:16,271 [pN:main.1,p:63>
Nov 30 11:43:16 bare-galaxy galaxyctl[6345]: galaxy.tools.search DEBUG 2023-11-30 11:43:16,278 [pN:main.1,p:63>
Nov 30 11:43:16 bare-galaxy galaxyctl[6345]: galaxy.tools.search DEBUG 2023-11-30 11:43:16,279 [pN:main.1,p:63>
Nov 30 11:43:16 bare-galaxy galaxyctl[6345]: galaxy.tools.search DEBUG 2023-11-30 11:43:16,285 [pN:main.1,p:63>

● galaxy-celery.service - Galaxy celery
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 11:42:48 UTC; 50s ago
   Main PID: 6305 (celery)
      Tasks: 2 (limit: 38496)
     Memory: 191.8M
        CPU: 7.279s
     CGroup: /system.slice/galaxy-celery.service
             ├─6305 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker --c>
             └─6342 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main(7)

Nov 30 11:42:55 bare-galaxy galaxyctl[6305]: [2023-11-30 11:42:55,248: INFO/MainProcess] Connected to sqlalche>
Nov 30 11:42:55 bare-galaxy galaxyctl[6305]: [2023-11-30 11:42:55,249: DEBUG/MainProcess] ^-- substep ok
Nov 30 11:42:55 bare-galaxy galaxyctl[6305]: [2023-11-30 11:42:55,249: DEBUG/MainProcess] | Consumer: Starting>
Nov 30 11:42:55 bare-galaxy galaxyctl[6305]: [2023-11-30 11:42:55,250: DEBUG/MainProcess] ^-- substep ok
Nov 30 11:42:55 bare-galaxy galaxyctl[6305]: [2023-11-30 11:42:55,250: DEBUG/MainProcess] | Consumer: Starting>
Nov 30 11:42:55 bare-galaxy galaxyctl[6305]: [2023-11-30 11:42:55,250: DEBUG/MainProcess] ^-- substep ok
Nov 30 11:42:55 bare-galaxy galaxyctl[6305]: [2023-11-30 11:42:55,250: DEBUG/MainProcess] | Consumer: Starting>
Nov 30 11:42:55 bare-galaxy galaxyctl[6305]: [2023-11-30 11:42:55,366: DEBUG/MainProcess] ^-- substep ok
Nov 30 11:42:55 bare-galaxy galaxyctl[6305]: [2023-11-30 11:42:55,366: DEBUG/MainProcess] | Consumer: Starting>
Nov 30 11:42:55 bare-galaxy galaxyctl[6305]: [2023-11-30 11:42:55,366: INFO/MainProcess] celery@bare-galaxy re>
lines 29-64/64 (END) ```

5 replies

slecrom Nov 30, 2023
Collaborator

Merci @Salimaiche

Salimaiche Nov 30, 2023

je ne peux pas faire de copier-coller mais voici l'erreur que j'ai eu pour le dernier outil.

slecrom Nov 30, 2023
Collaborator

Il s'agit d'un problème de copie de la clef API depuis le serveur Galaxy. Attention quand vous cliquez sur l'icône de copie une nouvelle fenêtre s'ouvre, il faut alors sélectionner la clef et ensuite la coller.

Salimaiche Dec 1, 2023

● galaxy-celery.service - Galaxy celery
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)
     Active: active (running) since Fri 2023-12-01 09:22:41 UTC; 35min ago
   Main PID: 666 (celery)
      Tasks: 3 (limit: 38496)
     Memory: 246.2M
        CPU: 35.130s
     CGroup: /system.slice/galaxy-celery.service
             ├─ 666 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker --c>
             └─1039 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main(7)

Dec 01 09:35:06 bare-galaxy galaxyctl[666]: [2023-12-01 09:35:06,640: INFO/main] Successfully executed Celery >
Dec 01 09:35:06 bare-galaxy galaxyctl[666]: [2023-12-01 09:35:06,640: INFO/main] Task galaxy.clean_object_stor>
Dec 01 09:45:07 bare-galaxy galaxyctl[666]: [2023-12-01 09:45:07,220: INFO/main] Task galaxy.clean_object_stor>
Dec 01 09:45:07 bare-galaxy galaxyctl[666]: [2023-12-01 09:45:07,220: DEBUG/main] TaskPool: Apply <function fa>
Dec 01 09:45:07 bare-galaxy galaxyctl[666]: [2023-12-01 09:45:07,222: INFO/main] Successfully executed Celery >
Dec 01 09:45:07 bare-galaxy galaxyctl[666]: [2023-12-01 09:45:07,223: INFO/main] Task galaxy.clean_object_stor>
Dec 01 09:55:06 bare-galaxy galaxyctl[666]: [2023-12-01 09:55:06,511: INFO/main] Task galaxy.clean_object_stor>
Dec 01 09:55:06 bare-galaxy galaxyctl[666]: [2023-12-01 09:55:06,512: DEBUG/main] TaskPool: Apply <function fa>
Dec 01 09:55:06 bare-galaxy galaxyctl[666]: [2023-12-01 09:55:06,513: INFO/main] Successfully executed Celery >
Dec 01 09:55:06 bare-galaxy galaxyctl[666]: [2023-12-01 09:55:06,514: INFO/main] Task galaxy.clean_object_stor>

● galaxy-gunicorn.service - Galaxy gunicorn
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)
     Active: active (running) since Fri 2023-12-01 09:22:41 UTC; 35min ago
   Main PID: 667 (gunicorn)
      Tasks: 16 (limit: 38496)
     Memory: 9.3G
        CPU: 26min 29.377s
     CGroup: /system.slice/galaxy-gunicorn.service
             ├─ 667 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_f>
             └─1040 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_f>

Dec 01 09:52:26 bare-galaxy galaxyctl[2644]:   samtools           bioconda/linux-64::samtools-1.9-h10a08f8_12
Dec 01 09:52:26 bare-galaxy galaxyctl[2644]:   xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Dec 01 09:52:26 bare-galaxy galaxyctl[2644]:   zlib               conda-forge/linux-64::zlib-1.2.13-hd590300_5
Dec 01 09:52:26 bare-galaxy galaxyctl[2644]:   zstd               conda-forge/linux-64::zstd-1.5.5-hfc55251_0
Dec 01 09:52:26 bare-galaxy galaxyctl[2644]: Preparing transaction: ...working... done
Dec 01 09:52:28 bare-galaxy galaxyctl[2644]: Verifying transaction: ...working... done
Dec 01 09:52:28 bare-galaxy galaxyctl[2644]: Executing transaction: ...working... done
Dec 01 09:52:28 bare-galaxy galaxyctl[1040]: galaxy.tool_util.deps DEBUG 2023-12-01 09:52:28,658 [pN:main.1,p:>
Dec 01 09:52:28 bare-galaxy galaxyctl[1040]: galaxy.tool_util.deps DEBUG 2023-12-01 09:52:28,659 [pN:main.1,p:>
Dec 01 09:52:28 bare-galaxy galaxyctl[1040]: uvicorn.access INFO 2023-12-01 09:52:28,705 [pN:main.1,p:1040,tN:>

● galaxy-celery-beat.service - Galaxy celery-beat
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)
     Active: active (running) since Fri 2023-12-01 09:22:41 UTC; 35min ago
   Main PID: 665 (celery)
      Tasks: 1 (limit: 38496)
     Memory: 207.2M
        CPU: 7.927s
     CGroup: /system.slice/galaxy-celery-beat.service
             └─665 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat --logl>

Dec 01 09:45:06 bare-galaxy galaxyctl[665]: [2023-12-01 09:45:06,384: DEBUG/MainProcess] beat: Synchronizing s>
Dec 01 09:45:06 bare-galaxy galaxyctl[665]: [2023-12-01 09:45:06,387: INFO/MainProcess] Scheduler: Sending due>
Dec 01 09:45:06 bare-galaxy galaxyctl[665]: [2023-12-01 09:45:06,398: DEBUG/MainProcess] galaxy.clean_object_s>
Dec 01 09:45:06 bare-galaxy galaxyctl[665]: [2023-12-01 09:45:06,399: DEBUG/MainProcess] beat: Waking up in 5.>
Dec 01 09:50:06 bare-galaxy galaxyctl[665]: [2023-12-01 09:50:06,499: DEBUG/MainProcess] beat: Synchronizing s>
Dec 01 09:50:06 bare-galaxy galaxyctl[665]: [2023-12-01 09:50:06,502: DEBUG/MainProcess] beat: Waking up in 5.>
Dec 01 09:55:06 bare-galaxy galaxyctl[665]: [2023-12-01 09:55:06,395: DEBUG/MainProcess] beat: Synchronizing s>
Dec 01 09:55:06 bare-galaxy galaxyctl[665]: [2023-12-01 09:55:06,397: INFO/MainProcess] Scheduler: Sending due>
Dec 01 09:55:06 bare-galaxy galaxyctl[665]: [2023-12-01 09:55:06,406: DEBUG/MainProcess] galaxy.clean_object_s>
Dec 01 09:55:06 bare-galaxy galaxyctl[665]: [2023-12-01 09:55:06,406: DEBUG/MainProcess] beat: Waking up in 5.>
lines 29-64/64 (END)```

Salimaiche Dec 1, 2023

        repository bedtools installed successfully (in 0:01:28.274331) at revision a1a923cd89e8
Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:26:57.017663``

zoeguilbert · 2023-11-30T13:13:33Z

zoeguilbert
Nov 30, 2023

root@bare-galaxy:~# systemctl status galaxy*.service                                                        
● galaxy-gunicorn.service - Galaxy gunicorn                                                                 
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)         
     Active: active (running) since Thu 2023-11-30 12:54:09 UTC; 16min ago                                  
   Main PID: 6251 (gunicorn)                                                                                
      Tasks: 14 (limit: 38496)                                                                              
     Memory: 463.8M                                                                                         
        CPU: 1min 17.945s                                                                                   
     CGroup: /system.slice/galaxy-gunicorn.service                                                          
             ├─6251 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fas>
             └─6289 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fas>
                                                                                                            
Nov 30 12:54:32 bare-galaxy galaxyctl[6289]: galaxy.tools.search DEBUG 2023-11-30 12:54:32,480 [pN:main.1,p>
Nov 30 12:54:32 bare-galaxy galaxyctl[6289]: galaxy.tools.search DEBUG 2023-11-30 12:54:32,481 [pN:main.1,p>
Nov 30 12:54:32 bare-galaxy galaxyctl[6289]: galaxy.tools.search DEBUG 2023-11-30 12:54:32,952 [pN:main.1,p>
Nov 30 12:54:32 bare-galaxy galaxyctl[6289]: galaxy.queue_worker INFO 2023-11-30 12:54:32,962 [pN:main.1,p:>
Nov 30 12:54:32 bare-galaxy galaxyctl[6289]: galaxy.tools.search DEBUG 2023-11-30 12:54:32,962 [pN:main.1,p>
Nov 30 12:54:32 bare-galaxy galaxyctl[6289]: galaxy.tools.search DEBUG 2023-11-30 12:54:32,968 [pN:main.1,p>
Nov 30 12:54:32 bare-galaxy galaxyctl[6289]: galaxy.tools.search DEBUG 2023-11-30 12:54:32,969 [pN:main.1,p>
Nov 30 12:54:32 bare-galaxy galaxyctl[6289]: galaxy.tools.search DEBUG 2023-11-30 12:54:32,973 [pN:main.1,p>
Nov 30 12:54:32 bare-galaxy galaxyctl[6289]: galaxy.tools.search DEBUG 2023-11-30 12:54:32,974 [pN:main.1,p>
Nov 30 12:54:32 bare-galaxy galaxyctl[6289]: galaxy.tools.search DEBUG 2023-11-30 12:54:32,978 [pN:main.1,p>

● galaxy-celery-beat.service - Galaxy celery-beat
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 12:54:09 UTC; 16min ago
   Main PID: 6249 (celery)
      Tasks: 1 (limit: 38496)
     Memory: 187.1M
        CPU: 6.133s
     CGroup: /system.slice/galaxy-celery-beat.service
             └─6249 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat -->

Nov 30 12:54:15 bare-galaxy galaxyctl[6249]: [2023-11-30 12:54:15,792: DEBUG/MainProcess] beat: Ticking wit>
Nov 30 12:54:15 bare-galaxy galaxyctl[6249]: [2023-11-30 12:54:15,794: DEBUG/MainProcess] beat: Waking up i>
Nov 30 12:59:15 bare-galaxy galaxyctl[6249]: [2023-11-30 12:59:15,894: DEBUG/MainProcess] beat: Synchronizi>
Nov 30 12:59:15 bare-galaxy galaxyctl[6249]: [2023-11-30 12:59:15,897: DEBUG/MainProcess] beat: Waking up i>
Nov 30 13:04:15 bare-galaxy galaxyctl[6249]: [2023-11-30 13:04:15,862: DEBUG/MainProcess] beat: Synchronizi>
Nov 30 13:04:15 bare-galaxy galaxyctl[6249]: [2023-11-30 13:04:15,873: INFO/MainProcess] Scheduler: Sending>
Nov 30 13:04:15 bare-galaxy galaxyctl[6249]: [2023-11-30 13:04:15,915: DEBUG/MainProcess] galaxy.clean_obje>
Nov 30 13:04:15 bare-galaxy galaxyctl[6249]: [2023-11-30 13:04:15,916: DEBUG/MainProcess] beat: Waking up i>
Nov 30 13:09:16 bare-galaxy galaxyctl[6249]: [2023-11-30 13:09:16,016: DEBUG/MainProcess] beat: Synchronizi>
Nov 30 13:09:16 bare-galaxy galaxyctl[6249]: [2023-11-30 13:09:16,018: DEBUG/MainProcess] beat: Waking up i>

● galaxy-celery.service - Galaxy celery
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 12:54:09 UTC; 16min ago
   Main PID: 6250 (celery)
      Tasks: 3 (limit: 38496)
     Memory: 229.4M
        CPU: 18.628s
     CGroup: /system.slice/galaxy-celery.service
             ├─6250 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker >
             └─6287 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main>

Nov 30 13:04:17 bare-galaxy galaxyctl[6250]: [2023-11-30 13:04:17,760: DEBUG/main] Loaded build site 'ensem>
Nov 30 13:04:17 bare-galaxy galaxyctl[6250]: [2023-11-30 13:04:17,760: DEBUG/main] Loaded build site 'ensem>
Nov 30 13:04:17 bare-galaxy galaxyctl[6250]: [2023-11-30 13:04:17,760: DEBUG/main] Build site file [tool-da>
Nov 30 13:04:17 bare-galaxy galaxyctl[6250]: [2023-11-30 13:04:17,760: DEBUG/main] Loaded build site 'igv':>
Nov 30 13:04:17 bare-galaxy galaxyctl[6250]: [2023-11-30 13:04:17,760: DEBUG/main] Build site file [tool-da>
Nov 30 13:04:17 bare-galaxy galaxyctl[6250]: [2023-11-30 13:04:17,760: DEBUG/main] Loaded build site 'rview>
Nov 30 13:04:17 bare-galaxy galaxyctl[6250]: [2023-11-30 13:04:17,763: DEBUG/main] Loading references to to>
Nov 30 13:04:17 bare-galaxy galaxyctl[6250]: [2023-11-30 13:04:17,763: DEBUG/main] Loaded reference to tool>
Nov 30 13:04:17 bare-galaxy galaxyctl[6250]: [2023-11-30 13:04:17,764: INFO/main] Successfully executed Cel>
Nov 30 13:04:17 bare-galaxy galaxyctl[6250]: [2023-11-30 13:04:17,773: INFO/main] Task galaxy.clean_object_>
lines 6-64/64 (END)

1 reply

zoeguilbert Nov 30, 2023

(.venv) root@bare-galaxy:~# tail -f tools.log
        repository samtool_filter2 installed successfully (in 0:00:32.854351) at revision 649a225999a5
(26/27) Installing repository sambamba from artbio to section "Samtools" at revision de833cc76a8e (TRT: 0:25:42.326286)
        repository sambamba installed successfully (in 0:00:44.841253) at revision de833cc76a8e
(27/27) Installing repository bedtools from iuc to section "Bedtools" at revision a1a923cd89e8 (TRT: 0:26:27.167870)
        repository bedtools installed successfully (in 0:01:26.967373) at revision a1a923cd89e8
Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:27:54.135809

LaurineBourel · 2023-11-30T13:21:26Z

LaurineBourel
Nov 30, 2023

laurine_bourel77@bare-galaxy:~$ systemctl status galaxy*.service
● galaxy-celery-beat.service - Galaxy celery-beat
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 12:47:57 UTC; 29min ago
   Main PID: 18478 (celery)
      Tasks: 1 (limit: 38496)
     Memory: 184.6M
        CPU: 5.933s
     CGroup: /system.slice/galaxy-celery-beat.service
             └─18478 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat --lo>

Nov 30 12:58:04 bare-galaxy galaxyctl[18478]: [2023-11-30 12:58:04,691: DEBUG/MainProcess] galaxy.clean_object>
Nov 30 12:58:04 bare-galaxy galaxyctl[18478]: [2023-11-30 12:58:04,692: DEBUG/MainProcess] beat: Waking up in >
Nov 30 13:03:04 bare-galaxy galaxyctl[18478]: [2023-11-30 13:03:04,764: DEBUG/MainProcess] beat: Synchronizing>
Nov 30 13:03:04 bare-galaxy galaxyctl[18478]: [2023-11-30 13:03:04,767: DEBUG/MainProcess] beat: Waking up in >
Nov 30 13:08:04 bare-galaxy galaxyctl[18478]: [2023-11-30 13:08:04,743: DEBUG/MainProcess] beat: Synchronizing>
Nov 30 13:08:04 bare-galaxy galaxyctl[18478]: [2023-11-30 13:08:04,746: INFO/MainProcess] Scheduler: Sending d>
Nov 30 13:08:04 bare-galaxy galaxyctl[18478]: [2023-11-30 13:08:04,757: DEBUG/MainProcess] galaxy.clean_object>
Nov 30 13:08:04 bare-galaxy galaxyctl[18478]: [2023-11-30 13:08:04,757: DEBUG/MainProcess] beat: Waking up in >
Nov 30 13:13:04 bare-galaxy galaxyctl[18478]: [2023-11-30 13:13:04,764: DEBUG/MainProcess] beat: Synchronizing>
Nov 30 13:13:04 bare-galaxy galaxyctl[18478]: [2023-11-30 13:13:04,766: DEBUG/MainProcess] beat: Waking up in >

● galaxy-celery.service - Galaxy celery
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 12:47:57 UTC; 29min ago
   Main PID: 18479 (celery)
      Tasks: 3 (limit: 38496)
     Memory: 231.9M
        CPU: 26.024s
     CGroup: /system.slice/galaxy-celery.service
             ├─18479 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker -->
             └─18516 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main(7)

Nov 30 12:58:06 bare-galaxy galaxyctl[18479]: [2023-11-30 12:58:06,385: DEBUG/main] Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.t>
Nov 30 12:58:06 bare-galaxy galaxyctl[18479]: [2023-11-30 12:58:06,388: DEBUG/main] Loading references to tool sheds from internal default config
Nov 30 12:58:06 bare-galaxy galaxyctl[18479]: [2023-11-30 12:58:06,389: DEBUG/main] Loaded reference to tool shed: Galaxy Main Tool Shed
Nov 30 12:58:06 bare-galaxy galaxyctl[18479]: [2023-11-30 12:58:06,389: INFO/main] Successfully executed Celery task clean_object_store_caches to prune object >
Nov 30 12:58:06 bare-galaxy galaxyctl[18479]: [2023-11-30 12:58:06,399: INFO/main] Task galaxy.clean_object_store_caches[12a06c62-1002-4441-b0dd-72b678cd127a] >
Nov 30 13:08:05 bare-galaxy galaxyctl[18479]: [2023-11-30 13:08:05,152: INFO/main] Task galaxy.clean_object_store_caches[cf20b8c2-e827-4ebd-9e68-45c22a6d41a4] >
Nov 30 13:08:05 bare-galaxy galaxyctl[18479]: [2023-11-30 13:08:05,152: DEBUG/main] TaskPool: Apply <function fast_trace_task at 0x7f7ae352e550> (args:('galaxy>
Nov 30 13:08:05 bare-galaxy galaxyctl[18479]: [2023-11-30 13:08:05,154: INFO/main] Successfully executed Celery task clean_object_store_caches to prune object >
Nov 30 13:08:05 bare-galaxy galaxyctl[18479]: [2023-11-30 13:08:05,154: INFO/main] Task galaxy.clean_object_store_caches[cf20b8c2-e827-4ebd-9e68-45c22a6d41a4] >

● galaxy-gunicorn.service - Galaxy gunicorn
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 12:47:57 UTC; 29min ago
   Main PID: 18480 (gunicorn)
      Tasks: 15 (limit: 38496)
     Memory: 473.3M
        CPU: 1min 59.604s
     CGroup: /system.slice/galaxy-gunicorn.service
             ├─18480 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib >
             └─18519 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib >

Nov 30 12:48:21 bare-galaxy galaxyctl[18519]: galaxy.tools.search DEBUG 2023-11-30 12:48:21,304 [pN:main.1,p:18519,tN:Thread-1] Toolbox index of panel ontology>
Nov 30 12:48:21 bare-galaxy galaxyctl[18519]: galaxy.queue_worker INFO 2023-11-30 12:48:21,322 [pN:main.1,p:18519,tN:Thread-1] Instance 'main.1' received 'rebu>
Nov 30 12:48:21 bare-galaxy galaxyctl[18519]: galaxy.tools.search DEBUG 2023-11-30 12:48:21,322 [pN:main.1,p:18519,tN:Thread-1] Starting to build toolbox index>
Nov 30 12:48:21 bare-galaxy galaxyctl[18519]: galaxy.tools.search DEBUG 2023-11-30 12:48:21,329 [pN:main.1,p:18519,tN:Thread-1] Toolbox index of panel default >
Nov 30 12:48:21 bare-galaxy galaxyctl[18519]: galaxy.tools.search DEBUG 2023-11-30 12:48:21,329 [pN:main.1,p:18519,tN:Thread-1] Starting to build toolbox index>
Nov 30 12:48:21 bare-galaxy galaxyctl[18519]: galaxy.tools.search DEBUG 2023-11-30 12:48:21,334 [pN:main.1,p:18519,tN:Thread-1] Toolbox index of panel ontology>
Nov 30 12:48:21 bare-galaxy galaxyctl[18519]: galaxy.tools.search DEBUG 2023-11-30 12:48:21,334 [pN:main.1,p:18519,tN:Thread-1] Starting to build toolbox index>
Nov 30 12:48:21 bare-galaxy galaxyctl[18519]: galaxy.tools.search DEBUG 2023-11-30 12:48:21,339 [pN:main.1,p:18519,tN:Thread-1] Toolbox index of panel ontology>
Nov 30 12:57:07 bare-galaxy galaxyctl[18519]: uvicorn.access INFO 2023-11-30 12:57:07,343 [pN:main.1,p:18519,tN:MainThread] 188.166.71.161:58942 - "GET /Tempor>
Nov 30 12:57:07 bare-galaxy galaxyctl[18519]: uvicorn.access INFO 2023-11-30 12:57:07,368 [pN:main.1,p:18519,tN:MainThread] 188.166.71.161:58952 - "GET /Pages/>
~
lines 34-64/64 (END)

0 replies

lin-ch1 · 2023-11-30T16:55:52Z

lin-ch1
Nov 30, 2023

● galaxy-gunicorn.service - Galaxy gunicorn                                                                 
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)         
     Active: active (running) since Thu 2023-11-30 13:48:37 UTC; 13min ago                                  
   Main PID: 6216 (gunicorn)                                                                                
      Tasks: 14 (limit: 38496)                                                                              
     Memory: 463.5M                                                                                         
        CPU: 1min 3.265s                                                                                    
     CGroup: /system.slice/galaxy-gunicorn.service                                                          
             ├─6216 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fas>
             └─6256 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fas>

Nov 30 13:49:01 bare-galaxy galaxyctl[6256]: galaxy.tools.search DEBUG 2023-11-30 13:49:01,254 [pN:main.1,p>
Nov 30 13:49:01 bare-galaxy galaxyctl[6256]: galaxy.tools.search DEBUG 2023-11-30 13:49:01,255 [pN:main.1,p>
Nov 30 13:49:01 bare-galaxy galaxyctl[6256]: galaxy.tools.search DEBUG 2023-11-30 13:49:01,700 [pN:main.1,p>
Nov 30 13:49:01 bare-galaxy galaxyctl[6256]: galaxy.queue_worker INFO 2023-11-30 13:49:01,710 [pN:main.1,p:>
Nov 30 13:49:01 bare-galaxy galaxyctl[6256]: galaxy.tools.search DEBUG 2023-11-30 13:49:01,710 [pN:main.1,p>
Nov 30 13:49:01 bare-galaxy galaxyctl[6256]: galaxy.tools.search DEBUG 2023-11-30 13:49:01,716 [pN:main.1,p>
Nov 30 13:49:01 bare-galaxy galaxyctl[6256]: galaxy.tools.search DEBUG 2023-11-30 13:49:01,717 [pN:main.1,p>
Nov 30 13:49:01 bare-galaxy galaxyctl[6256]: galaxy.tools.search DEBUG 2023-11-30 13:49:01,722 [pN:main.1,p>
Nov 30 13:49:01 bare-galaxy galaxyctl[6256]: galaxy.tools.search DEBUG 2023-11-30 13:49:01,722 [pN:main.1,p>
Nov 30 13:49:01 bare-galaxy galaxyctl[6256]: galaxy.tools.search DEBUG 2023-11-30 13:49:01,727 [pN:main.1,p>

● galaxy-celery-beat.service - Galaxy celery-beat
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 13:48:37 UTC; 13min ago
   Main PID: 6214 (celery)
      Tasks: 1 (limit: 38496)
     Memory: 186.0M
        CPU: 5.966s
     CGroup: /system.slice/galaxy-celery-beat.service
             └─6214 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat -->

Nov 30 13:48:44 bare-galaxy galaxyctl[6214]: <ScheduleEntry: cleanup-expired-notifications galaxy.cleanup_e>
Nov 30 13:48:44 bare-galaxy galaxyctl[6214]: <ScheduleEntry: celery.backend_cleanup celery.backend_cleanup(>
Nov 30 13:48:44 bare-galaxy galaxyctl[6214]: [2023-11-30 13:48:44,114: DEBUG/MainProcess] beat: Ticking wit>
Nov 30 13:48:44 bare-galaxy galaxyctl[6214]: [2023-11-30 13:48:44,115: DEBUG/MainProcess] beat: Waking up i>
Nov 30 13:53:44 bare-galaxy galaxyctl[6214]: [2023-11-30 13:53:44,216: DEBUG/MainProcess] beat: Synchronizi>
Nov 30 13:53:44 bare-galaxy galaxyctl[6214]: [2023-11-30 13:53:44,218: DEBUG/MainProcess] beat: Waking up i>
Nov 30 13:58:44 bare-galaxy galaxyctl[6214]: [2023-11-30 13:58:44,189: DEBUG/MainProcess] beat: Synchronizi>
Nov 30 13:58:44 bare-galaxy galaxyctl[6214]: [2023-11-30 13:58:44,199: INFO/MainProcess] Scheduler: Sending>
Nov 30 13:58:44 bare-galaxy galaxyctl[6214]: [2023-11-30 13:58:44,235: DEBUG/MainProcess] galaxy.clean_obje>
Nov 30 13:58:44 bare-galaxy galaxyctl[6214]: [2023-11-30 13:58:44,236: DEBUG/MainProcess] beat: Waking up i>

● galaxy-celery.service - Galaxy celery
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 13:48:37 UTC; 13min ago
   Main PID: 6215 (celery)
      Tasks: 3 (limit: 38496)
     Memory: 230.3M
        CPU: 15.687s
     CGroup: /system.slice/galaxy-celery.service
             ├─6215 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker >
             └─6254 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main>

Nov 30 13:58:45 bare-galaxy galaxyctl[6215]: [2023-11-30 13:58:45,781: DEBUG/main] Loaded build site 'ensem>
Nov 30 13:58:45 bare-galaxy galaxyctl[6215]: [2023-11-30 13:58:45,782: DEBUG/main] Loaded build site 'ensem>
Nov 30 13:58:45 bare-galaxy galaxyctl[6215]: [2023-11-30 13:58:45,782: DEBUG/main] Build site file [tool-da>
Nov 30 13:58:45 bare-galaxy galaxyctl[6215]: [2023-11-30 13:58:45,782: DEBUG/main] Loaded build site 'igv':>
Nov 30 13:58:45 bare-galaxy galaxyctl[6215]: [2023-11-30 13:58:45,782: DEBUG/main] Build site file [tool-da>
Nov 30 13:58:45 bare-galaxy galaxyctl[6215]: [2023-11-30 13:58:45,782: DEBUG/main] Loaded build site 'rview>
Nov 30 13:58:45 bare-galaxy galaxyctl[6215]: [2023-11-30 13:58:45,783: DEBUG/main] Loading references to to>
Nov 30 13:58:45 bare-galaxy galaxyctl[6215]: [2023-11-30 13:58:45,783: DEBUG/main] Loaded reference to tool>
Nov 30 13:58:45 bare-galaxy galaxyctl[6215]: [2023-11-30 13:58:45,783: INFO/main] Successfully executed Cel>
Nov 30 13:58:45 bare-galaxy galaxyctl[6215]: [2023-11-30 13:58:45,792: INFO/main] Task galaxy.clean_object_>
lines 30-64/64 (END)

1 reply

lin-ch1 Nov 30, 2023

repository samtool_filter2 installed successfully (in 0:00:35.662618) at revision 649a225999a5
(26/27) Installing repository sambamba from artbio to section "Samtools" at revision de833cc76a8e (TRT: 0:26:19.099234)
        repository sambamba installed successfully (in 0:00:44.258018) at revision de833cc76a8e
(27/27) Installing repository bedtools from iuc to section "Bedtools" at revision a1a923cd89e8 (TRT: 0:27:03.357556)
        repository bedtools installed successfully (in 0:01:23.256771) at revision a1a923cd89e8
Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:28:26.614921

claudiamart1s · 2023-11-30T18:10:38Z

claudiamart1s
Nov 30, 2023

 galaxy-celery-beat.service - Galaxy celery-beat                                                                                                                                                                                                
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)                                                                                                                                           
     Active: active (running) since Thu 2023-11-30 18:01:58 UTC; 3min 33s ago                                                                                                                                                                    
   Main PID: 6237 (celery)                                                                                                                                                                                                                       
      Tasks: 1 (limit: 38496)                                                                                                                                                                                                                    
     Memory: 187.1M                                                                                                                                                                                                                              
        CPU: 6.132s                                                                                                                                                                                                                              
     CGroup: /system.slice/galaxy-celery-beat.service                                                                                                                                                                                            
             └─6237 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat --loglevel DEBUG --schedule /root/galaxy/database/gravity/celery-beat-schedule                                                          
                                                                                                                                                                                                                                                 
Nov 30 18:02:05 bare-galaxy galaxyctl[6237]: [2023-11-30 18:02:05,957: DEBUG/MainProcess] Setting default socket timeout to 30                                                                                                                   
Nov 30 18:02:05 bare-galaxy galaxyctl[6237]: [2023-11-30 18:02:05,958: INFO/MainProcess] beat: Starting...                                                                                                                                       
Nov 30 18:02:06 bare-galaxy galaxyctl[6237]: [2023-11-30 18:02:06,009: DEBUG/MainProcess] Current schedule:                                                                                                                                      
Nov 30 18:02:06 bare-galaxy galaxyctl[6237]: <ScheduleEntry: cleanup-short-term-storage galaxy.cleanup_short_term_storage() <freq: 1.00 hour>                                                                                                    
Nov 30 18:02:06 bare-galaxy galaxyctl[6237]: <ScheduleEntry: clean-object-store-caches galaxy.clean_object_store_caches() <freq: 10.00 minutes>                                                                                                  
Nov 30 18:02:06 bare-galaxy galaxyctl[6237]: <ScheduleEntry: cleanup-expired-notifications galaxy.cleanup_expired_notifications() <freq: 1.00 day>                                                                                               
Nov 30 18:02:06 bare-galaxy galaxyctl[6237]: <ScheduleEntry: prune-history-audit-table galaxy.prune_history_audit_table() <freq: 1.00 hour>                                                                                                      
Nov 30 18:02:06 bare-galaxy galaxyctl[6237]: <ScheduleEntry: celery.backend_cleanup celery.backend_cleanup() <crontab: 0 4 * * * (m/h/d/dM/MY)>                                                                                                  
Nov 30 18:02:06 bare-galaxy galaxyctl[6237]: [2023-11-30 18:02:06,009: DEBUG/MainProcess] beat: Ticking with max interval->5.00 minutes                                                                                                          
Nov 30 18:02:06 bare-galaxy galaxyctl[6237]: [2023-11-30 18:02:06,011: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.                                                                                                                       
                                                                                                                                                                                                                                                 
● galaxy-gunicorn.service - Galaxy gunicorn
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 18:01:58 UTC; 3min 33s ago
   Main PID: 6239 (gunicorn)
      Tasks: 14 (limit: 38496)
     Memory: 462.2M
        CPU: 31.517s
     CGroup: /system.slice/galaxy-gunicorn.service
             ├─6239 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b 0.0.0.0:80 --workers=1 --config python:>
             └─6276 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b 0.0.0.0:80 --workers=1 --config python:>

Nov 30 18:02:23 bare-galaxy galaxyctl[6276]: galaxy.tools.search DEBUG 2023-11-30 18:02:23,641 [pN:main.1,p:6276,tN:Thread-1] Toolbox index of panel ontology:edam_operations finished (426.778 ms)
Nov 30 18:02:23 bare-galaxy galaxyctl[6276]: galaxy.tools.search DEBUG 2023-11-30 18:02:23,642 [pN:main.1,p:6276,tN:Thread-1] Starting to build toolbox index of panel ontology:edam_topics.
Nov 30 18:02:24 bare-galaxy galaxyctl[6276]: galaxy.tools.search DEBUG 2023-11-30 18:02:24,097 [pN:main.1,p:6276,tN:Thread-1] Toolbox index of panel ontology:edam_topics finished (454.108 ms)
Nov 30 18:02:24 bare-galaxy galaxyctl[6276]: galaxy.queue_worker INFO 2023-11-30 18:02:24,107 [pN:main.1,p:6276,tN:Thread-1] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
Nov 30 18:02:24 bare-galaxy galaxyctl[6276]: galaxy.tools.search DEBUG 2023-11-30 18:02:24,107 [pN:main.1,p:6276,tN:Thread-1] Starting to build toolbox index of panel default.
Nov 30 18:02:24 bare-galaxy galaxyctl[6276]: galaxy.tools.search DEBUG 2023-11-30 18:02:24,114 [pN:main.1,p:6276,tN:Thread-1] Toolbox index of panel default finished (6.436 ms)
Nov 30 18:02:24 bare-galaxy galaxyctl[6276]: galaxy.tools.search DEBUG 2023-11-30 18:02:24,114 [pN:main.1,p:6276,tN:Thread-1] Starting to build toolbox index of panel ontology:edam_operations.
Nov 30 18:02:24 bare-galaxy galaxyctl[6276]: galaxy.tools.search DEBUG 2023-11-30 18:02:24,119 [pN:main.1,p:6276,tN:Thread-1] Toolbox index of panel ontology:edam_operations finished (5.394 ms)
Nov 30 18:02:24 bare-galaxy galaxyctl[6276]: galaxy.tools.search DEBUG 2023-11-30 18:02:24,120 [pN:main.1,p:6276,tN:Thread-1] Starting to build toolbox index of panel ontology:edam_topics.
Nov 30 18:02:24 bare-galaxy galaxyctl[6276]: galaxy.tools.search DEBUG 2023-11-30 18:02:24,125 [pN:main.1,p:6276,tN:Thread-1] Toolbox index of panel ontology:edam_topics finished (4.759 ms)

● galaxy-celery.service - Galaxy celery
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 18:01:58 UTC; 3min 33s ago
   Main PID: 6238 (celery)
      Tasks: 2 (limit: 38496)
     Memory: 191.3M
        CPU: 8.944s
     CGroup: /system.slice/galaxy-celery.service
             ├─6238 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker --concurrency 2 --loglevel DEBUG --pool threads --queues celery,galaxy.internal,galaxy.external
             └─6275 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main(7)

Nov 30 18:02:06 bare-galaxy galaxyctl[6238]: [2023-11-30 18:02:06,069: INFO/MainProcess] Connected to sqlalchemy+sqlite:////root/galaxy/database/control.sqlite
Nov 30 18:02:06 bare-galaxy galaxyctl[6238]: [2023-11-30 18:02:06,069: DEBUG/MainProcess] ^-- substep ok
Nov 30 18:02:06 bare-galaxy galaxyctl[6238]: [2023-11-30 18:02:06,069: DEBUG/MainProcess] | Consumer: Starting Events
Nov 30 18:02:06 bare-galaxy galaxyctl[6238]: [2023-11-30 18:02:06,070: DEBUG/MainProcess] ^-- substep ok
Nov 30 18:02:06 bare-galaxy galaxyctl[6238]: [2023-11-30 18:02:06,070: DEBUG/MainProcess] | Consumer: Starting Tasks
Nov 30 18:02:06 bare-galaxy galaxyctl[6238]: [2023-11-30 18:02:06,174: DEBUG/MainProcess] ^-- substep ok
Nov 30 18:02:06 bare-galaxy galaxyctl[6238]: [2023-11-30 18:02:06,174: DEBUG/MainProcess] | Consumer: Starting Heart
Nov 30 18:02:06 bare-galaxy galaxyctl[6238]: [2023-11-30 18:02:06,175: DEBUG/MainProcess] ^-- substep ok
Nov 30 18:02:06 bare-galaxy galaxyctl[6238]: [2023-11-30 18:02:06,175: DEBUG/MainProcess] | Consumer: Starting event loop
Nov 30 18:02:06 bare-galaxy galaxyctl[6238]: [2023-11-30 18:02:06,175: INFO/MainProcess] celery@bare-galaxy ready.

0 replies

JulieBirgel · 2023-11-30T21:18:24Z

JulieBirgel
Nov 30, 2023

root@bare-galaxy:~# systemctl status galaxy*.service
● galaxy-celery-beat.service - Galaxy celery-beat
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 21:11:02 UTC; 2min 46s ago
   Main PID: 6572 (celery)
      Tasks: 1 (limit: 38496)
     Memory: 184.9M
        CPU: 6.465s
     CGroup: /system.slice/galaxy-celery-beat.service
             └─6572 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat --loglevel DEBUG --schedule /root/galaxy/database/gravity/celery-beat-schedule

Nov 30 21:11:09 bare-galaxy galaxyctl[6572]: [2023-11-30 21:11:09,697: DEBUG/MainProcess] Setting default socket timeout to 30
Nov 30 21:11:09 bare-galaxy galaxyctl[6572]: [2023-11-30 21:11:09,697: INFO/MainProcess] beat: Starting...
Nov 30 21:11:09 bare-galaxy galaxyctl[6572]: [2023-11-30 21:11:09,743: DEBUG/MainProcess] Current schedule:
Nov 30 21:11:09 bare-galaxy galaxyctl[6572]: <ScheduleEntry: prune-history-audit-table galaxy.prune_history_audit_table() <freq: 1.00 hour>
Nov 30 21:11:09 bare-galaxy galaxyctl[6572]: <ScheduleEntry: cleanup-expired-notifications galaxy.cleanup_expired_notifications() <freq: 1.00 day>
Nov 30 21:11:09 bare-galaxy galaxyctl[6572]: <ScheduleEntry: clean-object-store-caches galaxy.clean_object_store_caches() <freq: 10.00 minutes>
Nov 30 21:11:09 bare-galaxy galaxyctl[6572]: <ScheduleEntry: cleanup-short-term-storage galaxy.cleanup_short_term_storage() <freq: 1.00 hour>
Nov 30 21:11:09 bare-galaxy galaxyctl[6572]: <ScheduleEntry: celery.backend_cleanup celery.backend_cleanup() <crontab: 0 4 * * * (m/h/d/dM/MY)>
Nov 30 21:11:09 bare-galaxy galaxyctl[6572]: [2023-11-30 21:11:09,744: DEBUG/MainProcess] beat: Ticking with max interval->5.00 minutes
Nov 30 21:11:09 bare-galaxy galaxyctl[6572]: [2023-11-30 21:11:09,745: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.

● galaxy-celery.service - Galaxy celery
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 21:11:02 UTC; 2min 46s ago
   Main PID: 6573 (celery)
      Tasks: 2 (limit: 38496)
     Memory: 192.0M
        CPU: 8.972s
     CGroup: /system.slice/galaxy-celery.service
             ├─6573 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker --concurrency 2 --loglevel DEBUG --pool threads --queues celery,galaxy.internal,galaxy.external
             └─6612 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main(7)

Nov 30 21:11:09 bare-galaxy galaxyctl[6573]: [2023-11-30 21:11:09,801: INFO/MainProcess] Connected to sqlalchemy+sqlite:////root/galaxy/database/control.sqlite
Nov 30 21:11:09 bare-galaxy galaxyctl[6573]: [2023-11-30 21:11:09,801: DEBUG/MainProcess] ^-- substep ok
Nov 30 21:11:09 bare-galaxy galaxyctl[6573]: [2023-11-30 21:11:09,801: DEBUG/MainProcess] | Consumer: Starting Events
Nov 30 21:11:09 bare-galaxy galaxyctl[6573]: [2023-11-30 21:11:09,802: DEBUG/MainProcess] ^-- substep ok
Nov 30 21:11:09 bare-galaxy galaxyctl[6573]: [2023-11-30 21:11:09,802: DEBUG/MainProcess] | Consumer: Starting Heart
Nov 30 21:11:09 bare-galaxy galaxyctl[6573]: [2023-11-30 21:11:09,802: DEBUG/MainProcess] ^-- substep ok
Nov 30 21:11:09 bare-galaxy galaxyctl[6573]: [2023-11-30 21:11:09,803: DEBUG/MainProcess] | Consumer: Starting Tasks
Nov 30 21:11:09 bare-galaxy galaxyctl[6573]: [2023-11-30 21:11:09,902: DEBUG/MainProcess] ^-- substep ok
Nov 30 21:11:09 bare-galaxy galaxyctl[6573]: [2023-11-30 21:11:09,903: DEBUG/MainProcess] | Consumer: Starting event loop
Nov 30 21:11:09 bare-galaxy galaxyctl[6573]: [2023-11-30 21:11:09,903: INFO/MainProcess] celery@bare-galaxy ready.

● galaxy-gunicorn.service - Galaxy gunicorn
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 21:11:02 UTC; 2min 46s ago
   Main PID: 6574 (gunicorn)
      Tasks: 15 (limit: 38496)
     Memory: 475.2M
        CPU: 30.508s
     CGroup: /system.slice/galaxy-gunicorn.service
             ├─6574 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b 0.0.0.0:80 --workers=1 --config>
             └─6617 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b 0.0.0.0:80 --workers=1 --config>

Nov 30 21:11:28 bare-galaxy galaxyctl[6617]: galaxy.queue_worker INFO 2023-11-30 21:11:28,540 [pN:main.1,p:6617,tN:Thread-1] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
Nov 30 21:11:28 bare-galaxy galaxyctl[6617]: galaxy.tools.search DEBUG 2023-11-30 21:11:28,540 [pN:main.1,p:6617,tN:Thread-1] Starting to build toolbox index of panel default.
Nov 30 21:11:28 bare-galaxy galaxyctl[6617]: galaxy.tools.search DEBUG 2023-11-30 21:11:28,547 [pN:main.1,p:6617,tN:Thread-1] Toolbox index of panel default finished (6.621 ms)
Nov 30 21:11:28 bare-galaxy galaxyctl[6617]: galaxy.tools.search DEBUG 2023-11-30 21:11:28,547 [pN:main.1,p:6617,tN:Thread-1] Starting to build toolbox index of panel ontology:edam_operations.
Nov 30 21:11:28 bare-galaxy galaxyctl[6617]: galaxy.tools.search DEBUG 2023-11-30 21:11:28,553 [pN:main.1,p:6617,tN:Thread-1] Toolbox index of panel ontology:edam_operations finished (5.488 ms)
Nov 30 21:11:28 bare-galaxy galaxyctl[6617]: galaxy.tools.search DEBUG 2023-11-30 21:11:28,553 [pN:main.1,p:6617,tN:Thread-1] Starting to build toolbox index of panel ontology:edam_topics.
Nov 30 21:11:28 bare-galaxy galaxyctl[6617]: galaxy.tools.search DEBUG 2023-11-30 21:11:28,558 [pN:main.1,p:6617,tN:Thread-1] Toolbox index of panel ontology:edam_topics finished (5.102 ms)
Nov 30 21:11:59 bare-galaxy galaxyctl[6617]: /root/galaxy/lib/galaxy/webapps/base/webapp.py:954: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - round>
Nov 30 21:11:59 bare-galaxy galaxyctl[6617]:   if hasattr(self.galaxy_session, "current_history"):
Nov 30 21:11:59 bare-galaxy galaxyctl[6617]: uvicorn.access INFO 2023-11-30 21:11:59,650 [pN:main.1,p:6617,tN:MainThread] 47.116.40.141:45624 - "GET / HTTP/1.1" 200
lines 8-64/64 (END)

1 reply

JulieBirgel Nov 30, 2023

root@bare-galaxy:~# tail -f tools.log
        repository samtool_filter2 installed successfully (in 0:00:34.931113) at revision 649a225999a5
(26/27) Installing repository sambamba from artbio to section "Samtools" at revision de833cc76a8e (TRT: 0:27:16.181671)
        repository sambamba installed successfully (in 0:00:50.674149) at revision de833cc76a8e
(27/27) Installing repository bedtools from iuc to section "Bedtools" at revision a1a923cd89e8 (TRT: 0:28:06.856147)
        repository bedtools installed successfully (in 0:01:37.009110) at revision a1a923cd89e8
Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:29:43.865888

LeilaNeu · 2023-11-30T22:18:09Z

LeilaNeu
Nov 30, 2023

galaxy-celery.service - Galaxy celery                                                                         
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)               
     Active: active (running) since Thu 2023-11-30 22:09:17 UTC; 2min 39s ago                                   
   Main PID: 6229 (celery)                                                                                      
      Tasks: 2 (limit: 38496)                                                                                   
     Memory: 192.6M                                                                                             
        CPU: 13.228s                                                                                            
     CGroup: /system.slice/galaxy-celery.service                                                                
             ├─6229 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker --co>
             └─6266 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main(7)

Nov 30 22:09:29 bare-galaxy galaxyctl[6229]: [2023-11-30 22:09:29,550: INFO/MainProcess] Connected to sqlalchem>
Nov 30 22:09:29 bare-galaxy galaxyctl[6229]: [2023-11-30 22:09:29,550: DEBUG/MainProcess] ^-- substep ok
Nov 30 22:09:29 bare-galaxy galaxyctl[6229]: [2023-11-30 22:09:29,550: DEBUG/MainProcess] | Consumer: Starting >
Nov 30 22:09:29 bare-galaxy galaxyctl[6229]: [2023-11-30 22:09:29,551: DEBUG/MainProcess] ^-- substep ok
Nov 30 22:09:29 bare-galaxy galaxyctl[6229]: [2023-11-30 22:09:29,551: DEBUG/MainProcess] | Consumer: Starting >
Nov 30 22:09:29 bare-galaxy galaxyctl[6229]: [2023-11-30 22:09:29,551: DEBUG/MainProcess] ^-- substep ok
Nov 30 22:09:29 bare-galaxy galaxyctl[6229]: [2023-11-30 22:09:29,551: DEBUG/MainProcess] | Consumer: Starting >
Nov 30 22:09:29 bare-galaxy galaxyctl[6229]: [2023-11-30 22:09:29,694: DEBUG/MainProcess] ^-- substep ok
Nov 30 22:09:29 bare-galaxy galaxyctl[6229]: [2023-11-30 22:09:29,694: DEBUG/MainProcess] | Consumer: Starting >
Nov 30 22:09:29 bare-galaxy galaxyctl[6229]: [2023-11-30 22:09:29,695: INFO/MainProcess] celery@bare-galaxy rea>

● galaxy-celery-beat.service - Galaxy celery-beat
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 22:09:17 UTC; 2min 39s ago
   Main PID: 6228 (celery)
      Tasks: 1 (limit: 38496)
     Memory: 185.7M
        CPU: 11.270s
             └─6228 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat --loglevel DEBUG --schedule /root/galaxy/database/grav>

Nov 30 22:09:29 bare-galaxy galaxyctl[6228]: [2023-11-30 22:09:29,391: DEBUG/MainProcess] Setting default socket timeout to 30
Nov 30 22:09:29 bare-galaxy galaxyctl[6228]: [2023-11-30 22:09:29,392: INFO/MainProcess] beat: Starting...
Nov 30 22:09:29 bare-galaxy galaxyctl[6228]: [2023-11-30 22:09:29,445: DEBUG/MainProcess] Current schedule:
Nov 30 22:09:29 bare-galaxy galaxyctl[6228]: <ScheduleEntry: cleanup-expired-notifications galaxy.cleanup_expired_notifications() <freq: 1.00 day>
Nov 30 22:09:29 bare-galaxy galaxyctl[6228]: <ScheduleEntry: cleanup-short-term-storage galaxy.cleanup_short_term_storage() <freq: 1.00 hour>
Nov 30 22:09:29 bare-galaxy galaxyctl[6228]: <ScheduleEntry: prune-history-audit-table galaxy.prune_history_audit_table() <freq: 1.00 hour>
Nov 30 22:09:29 bare-galaxy galaxyctl[6228]: <ScheduleEntry: clean-object-store-caches galaxy.clean_object_store_caches() <freq: 10.00 minutes>
Nov 30 22:09:29 bare-galaxy galaxyctl[6228]: <ScheduleEntry: celery.backend_cleanup celery.backend_cleanup() <crontab: 0 4 * * * (m/h/d/dM/MY)>
Nov 30 22:09:29 bare-galaxy galaxyctl[6228]: [2023-11-30 22:09:29,446: DEBUG/MainProcess] beat: Ticking with max interval->5.00 minutes
Nov 30 22:09:29 bare-galaxy galaxyctl[6228]: [2023-11-30 22:09:29,447: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.

● galaxy-gunicorn.service - Galaxy gunicorn
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)
     Active: active (running) since Thu 2023-11-30 22:09:17 UTC; 2min 39s ago
   Main PID: 6230 (gunicorn)
      Tasks: 14 (limit: 38496)
     Memory: 464.0M
        CPU: 38.570s
     CGroup: /system.slice/galaxy-gunicorn.service
             ├─6230 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib ->
             └─6267 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_factory:factory() --timeout 300 --pythonpath lib ->

Nov 30 22:09:55 bare-galaxy galaxyctl[6267]: galaxy.tools.search DEBUG 2023-11-30 22:09:55,850 [pN:main.1,p:6267,tN:Thread-1] Toolbox index of panel ontology:e>
Nov 30 22:09:55 bare-galaxy galaxyctl[6267]: galaxy.tools.search DEBUG 2023-11-30 22:09:55,852 [pN:main.1,p:6267,tN:Thread-1] Starting to build toolbox index o>
Nov 30 22:09:56 bare-galaxy galaxyctl[6267]: galaxy.tools.search DEBUG 2023-11-30 22:09:56,290 [pN:main.1,p:6267,tN:Thread-1] Toolbox index of panel ontology:e>
Nov 30 22:09:56 bare-galaxy galaxyctl[6267]: galaxy.queue_worker INFO 2023-11-30 22:09:56,301 [pN:main.1,p:6267,tN:Thread-1] Instance 'main.1' received 'rebuil>
Nov 30 22:09:56 bare-galaxy galaxyctl[6267]: galaxy.tools.search DEBUG 2023-11-30 22:09:56,301 [pN:main.1,p:6267,tN:Thread-1] Starting to build toolbox index o>
Nov 30 22:09:56 bare-galaxy galaxyctl[6267]: galaxy.tools.search DEBUG 2023-11-30 22:09:56,309 [pN:main.1,p:6267,tN:Thread-1] Toolbox index of panel default fi>
Nov 30 22:09:56 bare-galaxy galaxyctl[6267]: galaxy.tools.search DEBUG 2023-11-30 22:09:56,309 [pN:main.1,p:6267,tN:Thread-1] Starting to build toolbox index o>
Nov 30 22:09:56 bare-galaxy galaxyctl[6267]: galaxy.tools.search DEBUG 2023-11-30 22:09:56,314 [pN:main.1,p:6267,tN:Thread-1] Toolbox index of panel ontology:e>
Nov 30 22:09:56 bare-galaxy galaxyctl[6267]: galaxy.tools.search DEBUG 2023-11-30 22:09:56,315 [pN:main.1,p:6267,tN:Thread-1] Starting to build toolbox index o>
Nov 30 22:09:56 bare-galaxy galaxyctl[6267]: galaxy.tools.search DEBUG 2023-11-30 22:09:56,320 [pN:main.1,p:6267,tN:Thread-1] Toolbox index of panel ontology:e>

1 reply

LeilaNeu Dec 1, 2023

Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:29:37.615758

SabineVautier · 2023-12-01T08:03:06Z

SabineVautier
Dec 1, 2023

(.venv) root@bare-galaxy:~# tail -f tools.log
        repository samtool_filter2 installed successfully (in 0:00:32.362887) at revision 649a225999a5
(26/27) Installing repository sambamba from artbio to section "Samtools" at revision de833cc76a8e (TRT: 0:24:49.275299)
        repository sambamba installed successfully (in 0:00:45.108476) at revision de833cc76a8e
(27/27) Installing repository bedtools from iuc to section "Bedtools" at revision a1a923cd89e8 (TRT: 0:25:34.384187)
        repository bedtools installed successfully (in 0:01:22.887993) at revision a1a923cd89e8
Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:26:57.272961

0 replies

LaurineBourel · 2023-12-01T08:43:45Z

LaurineBourel
Dec 1, 2023

(.venv) root@bare-galaxy:~# tail -f tools.log
(23/27) repository samtools_stats already installed at revision fed4aa48ba09. Skipping.
(24/27) repository samtools_view already installed at revision 6be888be75f9. Skipping.
(25/27) repository samtool_filter2 already installed at revision 649a225999a5. Skipping.
(26/27) repository sambamba already installed at revision de833cc76a8e. Skipping.
(27/27) repository bedtools already installed at revision a1a923cd89e8. Skipping.
Installed repositories (0): []
Skipped repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:00:13.924694

0 replies

claudiamart1s · 2023-12-01T15:55:36Z

claudiamart1s
Dec 1, 2023

(.venv) root@bare-galaxy:~# tail -f tools.log
        repository samtool_filter2 installed successfully (in 0:00:32.290346) at revision 649a225999a5
(26/27) Installing repository sambamba from artbio to section "Samtools" at revision de833cc76a8e (TRT: 0:25:52.159667)
        repository sambamba installed successfully (in 0:00:41.192876) at revision de833cc76a8e
(27/27) Installing repository bedtools from iuc to section "Bedtools" at revision a1a923cd89e8 (TRT: 0:26:33.353029)
        repository bedtools installed successfully (in 0:01:22.412619) at revision a1a923cd89e8
Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:27:55.766330

0 replies

camillejarry · 2023-12-03T15:14:45Z

camillejarry
Dec 3, 2023

root@bare-galaxy:~# systemctl status galaxy*.service
● galaxy-gunicorn.service - Galaxy gunicorn
     Loaded: loaded (/etc/systemd/system/galaxy-gunicorn.service; disabled; vendor preset: enabled)
     Active: active (running) since Sun 2023-12-03 15:01:35 UTC; 9min ago
   Main PID: 6206 (gunicorn)
      Tasks: 14 (limit: 38496)
     Memory: 464.7M
        CPU: 51.364s
     CGroup: /system.slice/galaxy-gunicorn.service
             ├─6206 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_f>
             └─6264 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/gunicorn galaxy.webapps.galaxy.fast_f>

Dec 03 15:02:00 bare-galaxy galaxyctl[6264]: galaxy.tools.search DEBUG 2023-12-03 15:02:00,046 [pN:main.1,p:62>
Dec 03 15:02:00 bare-galaxy galaxyctl[6264]: galaxy.tools.search DEBUG 2023-12-03 15:02:00,048 [pN:main.1,p:62>
Dec 03 15:02:00 bare-galaxy galaxyctl[6264]: galaxy.tools.search DEBUG 2023-12-03 15:02:00,477 [pN:main.1,p:62>
Dec 03 15:02:00 bare-galaxy galaxyctl[6264]: galaxy.queue_worker INFO 2023-12-03 15:02:00,488 [pN:main.1,p:626>
Dec 03 15:02:00 bare-galaxy galaxyctl[6264]: galaxy.tools.search DEBUG 2023-12-03 15:02:00,488 [pN:main.1,p:62>
Dec 03 15:02:00 bare-galaxy galaxyctl[6264]: galaxy.tools.search DEBUG 2023-12-03 15:02:00,495 [pN:main.1,p:62>
Dec 03 15:02:00 bare-galaxy galaxyctl[6264]: galaxy.tools.search DEBUG 2023-12-03 15:02:00,495 [pN:main.1,p:62>
Dec 03 15:02:00 bare-galaxy galaxyctl[6264]: galaxy.tools.search DEBUG 2023-12-03 15:02:00,500 [pN:main.1,p:62>
Dec 03 15:02:00 bare-galaxy galaxyctl[6264]: galaxy.tools.search DEBUG 2023-12-03 15:02:00,501 [pN:main.1,p:62>
Dec 03 15:02:00 bare-galaxy galaxyctl[6264]: galaxy.tools.search DEBUG 2023-12-03 15:02:00,506 [pN:main.1,p:62>

● galaxy-celery-beat.service - Galaxy celery-beat
     Loaded: loaded (/etc/systemd/system/galaxy-celery-beat.service; disabled; vendor preset: enabled)
     Active: active (running) since Sun 2023-12-03 15:01:35 UTC; 9min ago
   Main PID: 6204 (celery)
      Tasks: 1 (limit: 38496)
     Memory: 185.3M
        CPU: 6.057s
     CGroup: /system.slice/galaxy-celery-beat.service
             └─6204 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery beat --log>

Dec 03 15:01:42 bare-galaxy galaxyctl[6204]: [2023-12-03 15:01:42,123: DEBUG/MainProcess] Current schedule:
Dec 03 15:01:42 bare-galaxy galaxyctl[6204]: <ScheduleEntry: cleanup-short-term-storage galaxy.cleanup_short_t>
Dec 03 15:01:42 bare-galaxy galaxyctl[6204]: <ScheduleEntry: clean-object-store-caches galaxy.clean_object_sto>
Dec 03 15:01:42 bare-galaxy galaxyctl[6204]: <ScheduleEntry: cleanup-expired-notifications galaxy.cleanup_expi>
Dec 03 15:01:42 bare-galaxy galaxyctl[6204]: <ScheduleEntry: prune-history-audit-table galaxy.prune_history_au>
Dec 03 15:01:42 bare-galaxy galaxyctl[6204]: <ScheduleEntry: celery.backend_cleanup celery.backend_cleanup() <>
Dec 03 15:01:42 bare-galaxy galaxyctl[6204]: [2023-12-03 15:01:42,123: DEBUG/MainProcess] beat: Ticking with m>
Dec 03 15:01:42 bare-galaxy galaxyctl[6204]: [2023-12-03 15:01:42,124: DEBUG/MainProcess] beat: Waking up in 5>
Dec 03 15:06:42 bare-galaxy galaxyctl[6204]: [2023-12-03 15:06:42,182: DEBUG/MainProcess] beat: Synchronizing >
Dec 03 15:06:42 bare-galaxy galaxyctl[6204]: [2023-12-03 15:06:42,185: DEBUG/MainProcess] beat: Waking up in 5>

● galaxy-celery.service - Galaxy celery
     Loaded: loaded (/etc/systemd/system/galaxy-celery.service; disabled; vendor preset: enabled)
     Active: active (running) since Sun 2023-12-03 15:01:35 UTC; 9min ago
   Main PID: 6205 (celery)
      Tasks: 2 (limit: 38496)
     Memory: 193.4M
        CPU: 12.513s
     CGroup: /system.slice/galaxy-celery.service
             ├─6205 /root/galaxy/.venv/bin/python /root/galaxy/.venv/bin/celery --app galaxy.celery worker --c>
             └─6263 /root/galaxy/.venv/bin/python -c from multiprocessing.resource_tracker import main;main(7)

Dec 03 15:01:42 bare-galaxy galaxyctl[6205]: [2023-12-03 15:01:42,179: INFO/MainProcess] Connected to sqlalche>
Dec 03 15:01:42 bare-galaxy galaxyctl[6205]: [2023-12-03 15:01:42,179: DEBUG/MainProcess] ^-- substep ok
Dec 03 15:01:42 bare-galaxy galaxyctl[6205]: [2023-12-03 15:01:42,179: DEBUG/MainProcess] | Consumer: Starting>
Dec 03 15:01:42 bare-galaxy galaxyctl[6205]: [2023-12-03 15:01:42,179: DEBUG/MainProcess] ^-- substep ok
Dec 03 15:01:42 bare-galaxy galaxyctl[6205]: [2023-12-03 15:01:42,180: DEBUG/MainProcess] | Consumer: Starting>
Dec 03 15:01:42 bare-galaxy galaxyctl[6205]: [2023-12-03 15:01:42,279: DEBUG/MainProcess] ^-- substep ok
Dec 03 15:01:42 bare-galaxy galaxyctl[6205]: [2023-12-03 15:01:42,279: DEBUG/MainProcess] | Consumer: Starting>
Dec 03 15:01:42 bare-galaxy galaxyctl[6205]: [2023-12-03 15:01:42,279: DEBUG/MainProcess] ^-- substep ok
Dec 03 15:01:42 bare-galaxy galaxyctl[6205]: [2023-12-03 15:01:42,279: DEBUG/MainProcess] | Consumer: Starting>
Dec 03 15:01:42 bare-galaxy galaxyctl[6205]: [2023-12-03 15:01:42,280: INFO/MainProcess] celery@bare-galaxy re>
lines 27-64/64 (END)

3 replies

drosofff Dec 3, 2023
Maintainer Author

N'oubliez pas d'éteindre votre vm @camillejarry 😄

camillejarry Dec 3, 2023

(.venv) root@bare-galaxy:~# tail -f tools.log
        repository samtool_filter2 installed successfully (in 0:00:30.907862) at revision 649a225999a5
(26/27) Installing repository sambamba from artbio to section "Samtools" at revision de833cc76a8e (TRT: 0:23:08.305647)
        repository sambamba installed successfully (in 0:00:41.380231) at revision de833cc76a8e
(27/27) Installing repository bedtools from iuc to section "Bedtools" at revision a1a923cd89e8 (TRT: 0:23:49.686131)
        repository bedtools installed successfully (in 0:01:21.566100) at revision a1a923cd89e8
Installed repositories (27): [('data_manager_fetch_genome_dbkeys_all_fasta', '4d3eff1bc421'), ('data_manager_bowtie_index_builder', 'cb157f55b4fd'), ('sequence_format_converter', '1c14d2869d4d'), ('trimmomatic', '32f1f56bd970'), ('fastqc', '5ec9f6bceaee'), ('seqtk', '3da72230c066'), ('multiqc', 'abfd8a6544d7'), ('justdiff', '9299a59defda'), ('cherry_pick_fasta', 'ee689b6999d5'), ('text_processing', 'd698c222f354'), ('bowtie_wrappers', 'b46e7d48076a'), ('rseqc', '473382134e56'), ('featurecounts', 'f9d49f5cb597'), ('deseq2', '9a882d108833'), ('volcanoplot', '83c573f2e73c'), ('yac_clipper', '396bc2c718a1'), ('sr_bowtie', '3d5bd42097d7'), ('small_rna_maps', '966bc5c46efd'), ('small_rna_signatures', '5150d641d515'), ('sr_bowtie_dataset_annotation', 'fd4a60fc3fca'), ('weblogo3', 'dc25a5169a91'), ('samtools_sort', 'a577ea614bed'), ('samtools_stats', 'fed4aa48ba09'), ('samtools_view', '6be888be75f9'), ('samtool_filter2', '649a225999a5'), ('sambamba', 'de833cc76a8e'), ('bedtools', 'a1a923cd89e8')]
Skipped repositories (0): []
Errored repositories (0): []
All repositories have been installed.
Total run time: 0:25:11.252714

camillejarry Dec 3, 2023

La VM est bien arrêtée :)

Checking the deployment of your Galaxy server #29

drosofff Nov 21, 2023 Maintainer

Replies: 20 comments · 20 replies

drosofff Nov 27, 2023 Maintainer Author

drosofff Nov 27, 2023 Maintainer Author

drosofff Nov 27, 2023 Maintainer Author

slecrom Nov 30, 2023 Collaborator

slecrom Nov 30, 2023 Collaborator

drosofff Dec 3, 2023 Maintainer Author

drosofff
Nov 21, 2023
Maintainer

Replies: 20 comments 20 replies

drosofff Nov 27, 2023
Maintainer Author

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slecrom Nov 30, 2023
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slecrom Nov 30, 2023
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