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config.yaml
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config.yaml
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---
## Lines that must be updated when we release a new software version are
## indicated in comments below
output_dir: output
staging_deploy_root: [email protected]:/loc/www/bioconductor-test.fhcrc.org
production_deploy_root: [email protected]:/extra/www/bioc
## CHANGE THIS WHEN WE RELEASE A VERSION:
release_version: "3.17"
r_version_associated_with_release: "4.3.0"
r_version_associated_with_devel: "4.3.0"
## CHANGE THIS WHEN WE RELEASE A VERSION:
devel_version: "3.18"
## CHANGE THIS WHEN WE ADD A VERSION:
## This is the list of all versions for which we want to generate "new"
## bioc-views, package index, and package detail pages.
## if old versions (no older than 2.5) need to be rebuilt for any reason,
## add them here, but in most cases this should just contain the
## release and devel versions (though after a release you should
## let the no-longer-release version build one last time so package
## landing pages won't say "release version"):
versions:
- "3.17"
- "3.18"
## CHANGE THIS (i.e., uncomment) as various parts of the new devel version
## become available. set to "[]" if none are available.
devel_repos:
- "bioc"
- "data/experiment"
- "workflows"
- "data/annotation"
## CHANGE this when the build machines change:
## also, don't include machines that are not building yet (comment them out)
active_release_builders:
linux: "nebbiolo1"
windows: "palomino3"
mac_monterey: "merida1"
active_devel_builders:
linux: "nebbiolo2"
windows: "palomino4"
mac_monterey: "lconway"
## CHANGE this when the single package builder builds
## on a newer version of bioc
single_package_builder:
bioc_version: "3.18"
r_version: "4.3"
rss_hub_url: "https://pubsubhubbub.appspot.com/"
## CHANGE these as AMI IDS change
ami_ids:
bioc2_8: ami-3a2ef452
bioc2_9: ami-2623f94e
bioc2_10: ami-5621fb3e
bioc2_11: ami-f827fd90
bioc2_12: ami-7224fe1a
bioc2_13: ami-4a25ff22
bioc2_14: ami-9c25fff4
bioc3_0: ami-be7917d6
bioc3_1: ami-a3d126c8
bioc3_2: ami-85d88de0
bioc3_3: ami-abd0b3bc
bioc3_4: ami-8946709f
bioc3_5: ami-279a315d
bioc3_6: ami-ac5df1d3
bioc3_7: ami-01bcd08e357360496
bioc3_8: ami-0565362d8bfb9cbed
bioc3_9: ami-0f5d1990d8c571cdf
bioc3_10: ami-0c5ab50ca03a54468
bioc3_11: ami-071b80cf0d8ca085c
bioc3_12: ami-04c69d122c1cf7e81
bioc3_13: ami-0e7efd11a6eab85a6
string_pattern_type: legacy
data_sources:
- items_root: /
layouts_root: /
type: filesystem_unified
identifier_type: legacy
encoding: utf-8
config:
encoding: utf-8
- items_root: /
type: biostar_list
identifier_type: legacy
encoding: utf-8
config:
gmane_rss_url: 'http://rss.gmane.org/messages/excerpts/gmane.science.biology.informatics.conductor'
cache_file: tmp/gmane_list_cache_file.yaml
encoding: utf-8
ttl: 10
- items_root: /help/bioc-views/package-pages
layouts_root: /
type: bioc_views
identifier_type: legacy
encoding: utf-8
config:
json_dir: "assets/packages/json"
encoding: utf-8
- items_root: /help/publications/papers/pubmed
type: pubmed_papers
identifier_type: legacy
encoding: utf-8
config:
cache_file: tmp/pubmed_cache_file.yaml
retmax: 20
ttl: 24
baseurl: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/
# queried database, e.g. "pubmed" or "pmc"; can be a vector
db: [pubmed, pmc]
term: bioconductor
# Sorting of query results. This one is database-specific; possible values include
# pubmed: pub+date, first+author, last+author, journal, title, relevance
# pmc: print+pub+date, electronic+pub+date, journal, pmc+live+date
# For default sorting leave this field out
sort: [ "", electronic+pub+date]
# CHANGE THIS when it becomes apparent which future versions of BioC will
# work with which versions of R:
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"
# 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"
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.org/
https_mirror_url: https://bioconductor.org/
rsync: secure_mirror_from_master
country_code: us
- Germany:
- institution: Department of Statistics, TU Dortmund
institution_url: https://www.statistik.tu-dortmund.de/
contact: Uwe Ligges
contact_email: [email protected]
mirror_url: http://bioconductor.statistik.tu-dortmund.de/
https_mirror_url: https://bioconductor.statistik.tu-dortmund.de/
rsync:
city: Dortmund
country_code: de
- institution: GWDG
institution_url: https://ftp.gwdg.de/
contact: Tim Ehlers and Steffen Klemer
contact_email: [email protected]
mirror_url: http://ftp.gwdg.de/pub/misc/bioconductor/
https_mirror_url: https://ftp.gwdg.de/pub/misc/bioconductor/
rsync: secure_mirror_from_master
city: Gottingen
country_code: de
- Japan:
- institution: The Institute of Statistical Mathematics
institution_url: https://www.ism.ac.jp/
contact: Keisuke Honda
contact_email: [email protected]
mirror_url: http://bioc.ism.ac.jp/
https_mirror_url: https://bioc.ism.ac.jp/
rsync: secure_mirror_from_master
country_code: jp
city: Tachikawa
- institution: RIKEN Advanced Center for Computing and Communication
institution_url: https://accc.riken.jp/en/
contact: Itoshi NIKAIDO, Ph.D.
contact_email: [email protected]
mirror_url: http://bioconductor.riken.jp/
https_mirror_url: https://bioconductor.riken.jp/
rsync: secure_mirror_from_master
country_code: jp
city: Wako
- China:
- institution: TUNA Mirror Site, Tsinghua University
institution_url: mirrors.tuna.tsinghua.edu.cn
contact: Miao Wang
contact_email: [email protected]
mirror_url: http://mirrors.tuna.tsinghua.edu.cn/bioconductor/
https_mirror_url: https://mirrors.tuna.tsinghua.edu.cn/bioconductor/
rsync: secure_mirror_from_master
country_code: cn
city: Peking
- institution: eScience Center, Nanjing University
institution_url: https://sci.nju.edu.cn/
contact: Ge Yao
contact_email: [email protected]
mirror_url: http://mirrors.nju.edu.cn/bioconductor/
https_mirror_url: https://mirrors.nju.edu.cn/bioconductor/
rsync: secure_mirror_from_master
city: Nanjing
country_code: cn
- institution: University of Science and Technology of China (USTC)
institution_url: https://ustc.edu.cn
contact: Linux User Group (LUG) @ USTC
contact_email: [email protected]
mirror_url: http://mirrors.ustc.edu.cn/
https_mirror_url: https://mirrors.ustc.edu.cn/
rsync: secure_mirror_from_master
city: Hefei Anhui
country_code: cn
- Norway:
- institution: University of Bergen
institution_url: https://www.uib.no/
contact: Trond Davidsen
contact_email: [email protected]
mirror_url: http://bioconductor.uib.no/
https_mirror_url: https://bioconductor.uib.no/
rsync: secure_mirror_from_master
city: Bergen
country_code: no
- Italy:
- institution: University of Pisa
institution_url: https://www.unipi.it/
contact: Fabio Pratelli
contact_email: [email protected]
mirror_url: http://bioconductor.unipi.it
https_mirror_url: https://bioconductor.unipi.it
rsync: secure_mirror_from_master
city: Pisa
country_code: it
- Korea:
- institution: CRAN Asia
institution_url: https://cran.asia
contact: Seongho Bae
contact_email: [email protected]
mirror_url: http://cran.asia
https_mirror_url: https://cran.asia
rsync: secure_mirror_from_master
city: Seoul
country_code: kr
- Australia:
- institution: AARNet Pty Ltd
institution_url: https://aarnet.edu.au
contact: AARNet Operations Center
contact_email: [email protected]
mirror_url: http://mirror.aarnet.edu.au/pub/bioconductor
https_mirror_url: https://mirror.aarnet.edu.au/pub/bioconductor
rsync: secure_mirror_from_master
city: Sydney
country_code: au
- Denmark:
- institution: dotsrc
institution_url: https://dotsrc.org/
contact: Anders Trier Olesen
contact_email: [email protected]
mirror_url: http://mirrors.dotsrc.org/bioconductor/
https_mirror_url: https://mirrors.dotsrc.org/bioconductor/
rsync: secure_mirror_from_master
city: Aalborg
country_code: dk
- Sweden:
- institution: Academic Computer Club Umea
institution_url: https://www.accum.se/
contact: FTP admins
contact_email: [email protected]
mirror_url: http://mirror.accum.se/mirror/bioconductor.org/
https_mirror_url: https://mirror.accum.se/mirror/bioconductor.org/
rsync: secure_mirror_from_master
city: Umea
country_code: se