integration of RE Galaxy #210
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galaxy-re VM didn't have a privileged user (e.g., debian) so we need to create one manually |
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RE instance requires a few changes in LoginForm.vue and therefore to find out a way how to integrate these into the playbook. |
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bohuzel budou konflikty v tpv_meta s #194 mozna muzu celej tpv meta odtud vzit a mergnout tam, ty si pak jen das rebase |
Nemyslim si, ze to bude az take hrozne. |
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@martindemko ok, tak na #194 prosim mrkni, je to ready na merge pokud tam neco neni rozbiteho s tou dedicnosti, co jsi zminoval vyse |
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| toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc | |||
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This file needs update/merge across all instances, e.g. on usegalaxy.cz there is fastp which is missing from here.
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| @charset "UTF-8";.markdown-textarea{border:1px solid #ccc;border-top:none;border-bottom:none;resize:none;outline:none;background-color:#f6f6f6;font-size:14px;font-family:Monaco,courier,monospace;padding:20px;width:100%;height:95%}pre code{white-space:pre-wrap}.badge{padding:.2em .6em .3em;border-width:1px;border-style:solid;border-radius:.15rem;text-decoration:none}.nametags:empty{display:none}.nametags .badge{display:inline-block;margin-right:2px}.galaxy-page-editor-button{position:relative;float:left;padding:.2em} | |||
| path: "{{ galaxy_root }}/server/lib/galaxy/webapps/galaxy/api/job_files.py" | ||
| regexp: '^(\s*?)shutil\.move\(input_file\.name,\s*path\)\s*$' | ||
| replace: '\1os.chmod(shutil.move(input_file.name, path), 0o664)' | ||
| - name: Set-up pre-defined integrated_tool_panel config file on RE instance only |
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this config is mutable, Galaxy will regenerate it, we should not preserve it in playbook
| dest: "{{ tpv_mutable_dir }}/tpv_rules_meta.yml" | ||
| - src: "templates/galaxy/config/vault_conf.yml.j2" | ||
| dest: "{{ galaxy_config_dir }}/vault_conf.yml" | ||
| - src: templates/galaxy/config/dependency_resolvers_conf.xml.j2 |
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Do we really need to juggle around empty files for instances that do not use dependency resolvers at all?
| dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}" | ||
| - src: "{{ lookup('first_found', ['templates/'+inventory_hostname+'/config/file_source_templates.yml.j2', 'templates/galaxy/config/file_source_templates.yml.j2']) }}" | ||
| dest: "{{ galaxy_config_dir }}/file_source_templates.yml" | ||
| - src: "{{ lookup('first_found', ['templates/'+inventory_hostname+'/config/auth_conf.xml.j2', 'templates/galaxy/config/auth_conf.xml.j2']) }}" |
| - /cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml | ||
| - /cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml | ||
| # Tool Dependencies | ||
| dependency_resolvers_config_file: "{{ galaxy_config_dir }}/dependency_resolvers_conf.xml" |
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can we just set this to empty for non-regalaxy?
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| proftpd | |||
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I believe changes to this role should go upstream, not into playbook. Is that feasible?
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| --- | |||
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I don't think this playbook is needed
| ansible_user: debian | ||
| galaxy-qa2.galaxy.cloud.e-infra.cz: | ||
| ansible_user: debian | ||
| galaxy-re.grid.cesnet.cz: |
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I thought we want one inventory item per host. Please document the reason for duplication between galaxy-re.grid and repeatexplorer-elixir and how will we approach the maintenance of such approach.
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As agreed I merged #194 -- please rebase this PR on top of it. @martindemko I left some comments inline, overall it feels close to finished. I think we should be able to merge and deploy on Monday. |
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