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Merge pull request #126 from hic-infra/r-bioconductor
Add reverse proxy for bioconductor (R)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -31,6 +31,20 @@ | |
| line: 127.0.0.1 conda.{{zone}} | ||
| unsafe_writes: true # issue with testing inside a container | ||
|
|
||
| - name: add testing endpoint to /etc/hosts | ||
| become: true | ||
| lineinfile: | ||
| path: /etc/hosts | ||
| line: 127.0.0.1 bioconductor.{{zone}} | ||
| unsafe_writes: true # issue with testing inside a container | ||
|
|
||
| - name: break access to bioconductor.org for testing | ||
| become: true | ||
| lineinfile: | ||
| path: /etc/hosts | ||
| line: 255.255.255.255 bioconductor.org | ||
| unsafe_writes: true # issue with testing inside a container | ||
|
|
||
| - name: install R for testing package installation | ||
| become: true | ||
| apt: | ||
|
|
@@ -73,3 +87,161 @@ | |
| channels: | ||
| - http://conda.{{ zone}}/conda-forge | ||
| ssl_verify: False | ||
| - name: create a bioconductor config for testing | ||
| copy: | ||
| dest: /root/config.yaml | ||
| content: | | ||
| --- | ||
| output_dir: output | ||
| staging_deploy_root: [email protected]:/loc/www/bioconductor-test-new | ||
| production_deploy_root: [email protected]:/extra/www/bioc | ||
| staging_dir: /loc/www/bioconductor-test-new | ||
| release_version: "3.19" | ||
| r_version_associated_with_release: "4.4.0" | ||
| r_version_associated_with_devel: "4.4.0" | ||
| devel_version: "3.20" | ||
| versions: | ||
| - "3.19" | ||
| - "3.20" | ||
| devel_repos: | ||
| - "bioc" | ||
| r_ver_for_bioc_ver: | ||
| "1.6": "2.1" | ||
| "1.7": "2.2" | ||
| "1.8": "2.3" | ||
| "1.9": "2.4" | ||
| "2.0": "2.5" | ||
| "2.1": "2.6" | ||
| "2.2": "2.7" | ||
| "2.3": "2.8" | ||
| "2.4": "2.9" | ||
| "2.5": "2.10" | ||
| "2.6": "2.11" | ||
| "2.7": "2.12" | ||
| "2.8": "2.13" | ||
| "2.9": "2.14" | ||
| "2.10": "2.15" | ||
| "2.11": "2.15" # R switching to yearly releases, BioC remaining the same | ||
| "2.12": "3.0" | ||
| "2.13": "3.0" | ||
| "2.14": "3.1" | ||
| "3.0": "3.1" | ||
| "3.1": "3.2" | ||
| "3.2": "3.2" | ||
| "3.3": "3.3" | ||
| "3.4": "3.3" | ||
| "3.5": "3.4" | ||
| "3.6": "3.4" | ||
| "3.7": "3.5" | ||
| "3.8": "3.5" | ||
| "3.9": "3.6" | ||
| "3.10": "3.6" | ||
| "3.11": "4.0" | ||
| "3.12": "4.0" | ||
| "3.13": "4.1" | ||
| "3.14": "4.1" | ||
| "3.15": "4.2" | ||
| "3.16": "4.2" | ||
| "3.17": "4.3" | ||
| "3.18": "4.3" | ||
| "3.19": "4.4" | ||
| "3.20": "4.4" | ||
| # UPDATE THIS when we release a version | ||
| release_dates: # old info from http://en.wikipedia.org/wiki/Bioconductor#Milestones | ||
| "1.0": "1/5/2001" | ||
| "1.1": "11/19/2002" | ||
| "1.2": "5/29/2003" | ||
| "1.3": "10/30/2003" | ||
| "1.4": "5/17/2004" | ||
| "1.5": "10/25/2004" | ||
| "1.6": "5/18/2005" | ||
| "1.7": "10/14/2005" | ||
| "1.8": "4/27/2006" | ||
| "1.9": "10/4/2006" | ||
| "2.0": "4/26/2007" | ||
| "2.1": "10/8/2007" | ||
| "2.2": "5/1/2008" | ||
| "2.3": "10/22/2008" | ||
| "2.4": "4/21/2009" | ||
| "2.5": "10/28/2009" | ||
| "2.6": "4/23/2010" | ||
| "2.7": "10/18/2010" | ||
| "2.8": "4/14/2011" | ||
| "2.9": "11/1/2011" | ||
| "2.10": "4/2/2012" | ||
| "2.11": "10/3/2012" | ||
| "2.12": "4/4/2013" | ||
| "2.13": "10/15/2013" | ||
| "2.14": "4/14/2014" | ||
| "3.0": "10/14/2014" | ||
| "3.1": "4/17/2015" | ||
| "3.2": "10/14/2015" | ||
| "3.3": "5/4/2016" | ||
| "3.4": "10/18/2016" | ||
| "3.5": "4/25/2017" | ||
| "3.6": "10/31/2017" | ||
| "3.7": "05/01/2018" | ||
| "3.8": "10/31/2018" | ||
| "3.9": "05/03/2019" | ||
| "3.10": "10/30/2019" | ||
| "3.11": "04/28/2020" | ||
| "3.12": "10/28/2020" | ||
| "3.13": "05/20/2021" | ||
| "3.14": "10/27/2021" | ||
| "3.15": "04/27/2022" | ||
| "3.16": "11/02/2022" | ||
| "3.17": "04/26/2023" | ||
| "3.18": "10/25/2023" | ||
| "3.19": "05/01/2024" | ||
| release_last_built_dates: | ||
| '2.0': 09/12/2007 | ||
| '2.1': 04/09/2008 | ||
| '2.2': 10/16/2008 | ||
| '2.3': 04/18/2009 | ||
| '2.4': 10/20/2009 | ||
| '2.5': 04/03/2010 | ||
| '2.6': 10/05/2010 | ||
| '2.7': 04/07/2011 | ||
| '2.8': 10/21/2011 | ||
| '2.9': 03/24/2012 | ||
| '2.10': 09/24/2012 | ||
| '2.11': 03/25/2013 | ||
| '2.12': 10/09/2013 | ||
| '2.13': 04/05/2014 | ||
| '2.14': 10/08/2014 | ||
| '3.0': 04/10/2015 | ||
| '3.1': 10/09/2015 | ||
| '3.2': 04/23/2016 | ||
| '3.3': 10/13/2016 | ||
| '3.4': 04/15/2017 | ||
| '3.5': 10/18/2017 | ||
| '3.6': 04/12/2018 | ||
| '3.7': 10/17/2018 | ||
| '3.8': 04/16/2019 | ||
| '3.9': 10/16/2019 | ||
| '3.10': 04/15/2020 | ||
| '3.11': 10/17/2020 | ||
| '3.12': 05/06/2021 | ||
| '3.13': 10/15/2021 | ||
| '3.14': 04/13/2022 | ||
| '3.15': 10/19/2022 | ||
| '3.16': 04/12/2023 | ||
| '3.17': 10/16/2023 | ||
| '3.18': 04/17/2024 | ||
| mirrors: | ||
| - 0-Bioconductor: | ||
| - institution: Bioconductor, automatic redirection to servers worldwide | ||
| institution_url: https://bioconductor.org | ||
| contact: Bioconductor Maintainer | ||
| contact_email: [email protected] | ||
| city: World-wide | ||
| mirror_url: http://bioconductor.localhost/ | ||
| #https_mirror_url: https://bioconductor.org/ | ||
| rsync: secure_mirror_from_master | ||
| country_code: us | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| --- | ||
|
|
||
| - name: add our bioconductor reverse proxy config | ||
| become: true | ||
| template: | ||
| dest: /etc/nginx/sites-enabled/bioconductor.conf | ||
| src: generic.conf.j2 | ||
| vars: | ||
| generic_name: bioconductor | ||
| upstream_endpoint: "{{ bioconductor_mirror }}" | ||
| eicar_path: packages/src/contrib/eicar.tar.gz | ||
| endpoint_regex: "{{ bioconductor_regex }}" | ||
| certificate_file: "{{ bioconductor_cert }}" | ||
| certificate_key_file: "{{ bioconductor_cert_key }}" | ||
| notify: restart nginx |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -13,4 +13,5 @@ | |
| state: absent | ||
|
|
||
| - include_tasks: cran.yml | ||
| - include_tasks: bioconductor.yml | ||
| - include_tasks: conda.yml | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -14,6 +14,6 @@ provisioner: | |
| group_vars: | ||
| all: | ||
| allowed_domains: | ||
| - dundee.ac.uk | ||
| - eu.httpbin.org | ||
| verifier: | ||
| name: ansible | ||