Speaker
Description
Hutch
Fred Hutch Cancer Research Center has about 230 scientific faculties and
just over 3,000 staff. Located in Seattle, Washington on a 15 Acre
Campus (60,702 M^2). We have an HPC group of 6 people and support 6
thousand core cluster on campus.
R
The Fred Hutch has hundreds of R users. Robert Gentleman who is one of
the co-developers of R worked at the Hutch while still actively
developing the language. Gentleman now works at 23andMe. Bioconductor
originated at the Fred Hutchinson Cancer Research Center in the Fall of
2001. Martin Morgan led Bioconductor development since 2008 joined the
Fred Hutch in 2005. The BioConductor group has since moved to Roswell
Park Cancer Center. R is the predominant language used by BioInformatics
staff at the Hutch. Our local R build has over 700 modules. Our HPC
group (me) has to devote considerable effort to maintain R for the center.
R Strategy
Our users want the latest version of R built as quickly as possible.
Using the foss-2018b toolchain, we will deploy the standard EB release
of R with a day of its Release. The Fred Hutch release of R will be
built as Bundle using the community release as a base. The Fred Hutch R
build has over 800 modules. Our local version of R has a version suffix
of "-fhX."
Easy_Update and Easy_Annotate
I am the author of easy_update. Easy_update is used to update package
versions for R and Python easyconfig recipes. Version information is
obtained from the respected package authority CRAN, PyPi, and
BioConductor. Easy_update resolves package dependencies.
Easy_Annotate documents our R and Python builds at the package level.
Fred Hutch uses GitHub pages to document our Easybuild scientific
software: https://urldefense.proofpoint.com/v2/url?u=https-3A__fredhutch.github.io_easybuild-2Dlife-2Dsciences_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=3TR-iteG1SyRqQ5yubQg-_2KIAToz9bj5dZrRdW36Hc&m=aKY87YplHcgIjHlZTGEyDTp23LoyK5aKhezrP87D0Y0&s=HDoEsgVW8-k4qfXW0pL4xEB3uL0wj73fJ6kVKN8rOho&e=
I plan to add the easy_update features to easybuild. Easy_update has
been under much change due to the move to PyPi and needing to support
Bioconductor packages for R., And I keep finding horrible bugs which I
would not want to in EasyBuild.
Future EB Plans
- We would like to benefit from foss-2018b library consistency
- We want to contribute packages to the community
- Have implemented a Docker build environment to ensure more consistent
and repeatable packages. GitHub: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.github.com_FredHutch_ls2&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=3TR-iteG1SyRqQ5yubQg-_2KIAToz9bj5dZrRdW36Hc&m=aKY87YplHcgIjHlZTGEyDTp23LoyK5aKhezrP87D0Y0&s=skrWOrz8DuoJ6VARpFoTtO1WH6KERpyuPQ0cHe_3Kvc&e= - Committed to foss-2018b toolchain for the next few years. Our site is
planning to upgrade our cluster to Ubuntu 18.04. - We meet people who are using EasyBuild but are not contributing back
to the community. We want to encourage more sites globally to
participate in making Scientific Software more accessible.
