galaxyXpand release_24.0

to adapt GalaxyXpand to release 24.0

Release_23.2

State of GalaxyXpand after Galaxy release_23.2 upgrade on all ARTbio Galaxy servers

release_23.1

What's Changed

• galaxyXpand simplification and consistency by @drosofff in #48

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• Gathering common variables in 000_cross_env_vars

• Merging common and specific galaxy_config dictionaries

• Update playbook.yml

• put conda default to 23.11

• add nginx_conf_user variable in the playbook (nginx role )

• nginx reverse proxy stays to port 4000 for dev_gce

• GALAXY release 23.1

• galaxy_manage_systemd "false" in docker group_vars

• simplification of gce and docker envs

• simplify env dev_mississippi

• simplify conect

• Update welcome.html.j2

• simplification of Mississippi environment

• Update welcome.html.j2

• fix Conect welcome page

• fix dev_mississippi welcome page

• simplification of ARTbio environment

galaxyXpand release_23.0

• target galaxy release_23.0

• Update test_playbook.yaml

• Update requirements.yml

• Update playbook.yml

• Update 000_cross_env_vars

• create a dbserver.yml "host"

• reorganize playbook in 2 hosts dbserver and all

• Update 000_cross_env_vars

• Update hosts

• add - 'virtualenv' in dependencies. Don't get why it's not in the GNT ansible training !

• change miniconda version !

and undo miniconda_manage_dependencies = false (commented)

• switch to job_conf.yml structure

• switch uptream galaxy on gunicorn.sock

• Update ansible.cfg

• tune group_vars galaxy and nginx

• Update .gitignore

• switch to ansible 3.0 and bioblend 1.2.0

• upgrade Docker role to release_23.0 and lint dev_gce

• add psql user galaxy in Dockerfile

• create galaxy psql db before ansible playbook

• remove nginx post task and tweek ansible-playbook

remove -c local from the ansible-playbook command in Dockerfile

• galaxy_manage_systemd is false by default

• Fixing bugged handler that crashes in docker

• upgrade dev_mississippi env to release_23.0

• let job_conf.yml as is in files

• Update job_conf.yml

• Update galaxy.j2

• remove job_conf and update slurm group_vars

• conf_job.yml Mississippi

• slurm conf of Mississippi

• Update mississippi_tool_list.yml

• Update Mississippi hosts file

• fix miniconda_channels Mississippi

• nginx Mississippi configuration

• Update dev_mississippi slurm group_vars

• adjust Mississippi slurm group_vars

• Update Mississippi job_conf.yml

• create an uptime service to replace uptime supervisor

• Update .gitignore

• Update Conect hosts

• Conect job_conf.yml

• Forgot create a simlink to dbservers.yml for Mississippi

So strangely enough it may be not required !

• conect template nginx/galaxy.j2

• Fix dev_mississippi welcome page

• fix mississippi_dev.png target location

• Update welcome page of Mississippi-2

• Update conect_tool_list.yml

• Update artbio_tool_list.yml

• Update ARTbio hosts

It seems that there was a bug in this config with [Conect] instead of [ARTbio] !

• Update ARTbio galaxy.j2

• Update artbio.snv.jussieu.fr.crt

There was a need to re-import the updated crt into this already old branch !

• Update welcome.html

test fastqc under java destination

• tune fastqc in Mississippi job_conf.yml

• 8 workers for Mississippi !

• 8 workers for ARTbio !

• test conda 3.11 for ARTbio

• Change the default destination of ARTbio to slurm cluster_1

• Change the default destination of Conect to slurm cluster_1

• Change the default destination of Mississippi[2] to slurm cluster_1