Development work should be done usually on the devel version of Bioconductor (3.12), which is in the bioconductor_docker:devel image.
The stable release, has the latest Bioconductor stable release version 3.11 on the image bioconductor_docker:RELEASE_3_11. Hope that answers your question. Best, Nitesh > On Aug 3, 2020, at 11:46 AM, Joseph Gerrein <gerrein.jos...@gene.com> wrote: > > Hi Nitesh, > > Thank you so much for that detailed explanation! I have just one > follow-up question – we are internally developing A wrapper for > MultiAssayExperiment. Do you recommend using the devel version or the > stable release version? > > Thanks, > > Joe > > On Mon, Aug 3, 2020 at 8:11 AM Nitesh Turaga <nturaga.b...@gmail.com> wrote: >> >> Hi Joesph, >> >> 1. The RELEASE_3_11 and devel images do not have any installed packages. You >> are free to install the packages within these images. Please read the help >> http://bioconductor.org/help/docker/. The goal behind these images is to >> provide an image where all Bioconductor packages can be installed. Once you >> install the MultiAssayExperiment package it will load just fine. >> >> 2. The RELEASE_3_11 image is the stable version, the devel version will keep >> changing every week based on updates in R and any fixes Bioconductor issues. >> >> 3. The bioconductor_docker:bioc2020 image is based on the ‘devel’ image, but >> a frozen tag during the conference. The docker images used for workshops >> come with pre-installed packages, and they are derived from the >> bioconductor/bioconductor_docker:devel image. >> >> I would recommend using the bioconductor/bioconductor_docker:RELEASE_3_11 >> (stable) image for analysis work. All images provided by Bioconductor are >> reliable. If you need to report any issues, please use the >> https://github.com/Bioconductor/bioconductor_docker/issues. >> >> Best, >> >> Nitesh >> >> On Aug 3, 2020, at 11:03 AM, Shepherd, Lori <lori.sheph...@roswellpark.org> >> wrote: >> >> Marcel or Nitesh? This was sent to the issue bot. >> >> >> >> >> Lori Shepherd >> >> Bioconductor Core Team >> >> Roswell Park Comprehensive Cancer Center >> >> Department of Biostatistics & Bioinformatics >> >> Elm & Carlton Streets >> >> Buffalo, New York 14263 >> >> ________________________________ >> From: Joseph Gerrein <gerrein.jos...@gene.com> >> Sent: Tuesday, July 28, 2020 11:03 AM >> To: bioc-issue-...@bioconductor.org <bioc-issue-...@bioconductor.org> >> Cc: Jerry (Zhijun) Tang <jt...@gene.com>; Lala Motlhabi <motlh...@gene.com> >> Subject: MultiAssayExperiment not found in docker devel image >> >> Dear bioconductor team, >> >> Hello! I would like to use MultiAssayExperiment in a preloaded bioconductor >> Docker container that does not require any package installations. I loaded >> the docker devel image and also the Docker release 3_11 image (from >> https://hub.docker.com/r/bioconductor/bioconductor_docker/tags<https://secure-web.cisco.com/1CBV0e1ECW2oH221MZYDrB6ZGZnORfj8i0E9oO6_S0_SuOZu0RxuZrxoZW9vYhbr2tTlHVmXyKmcJ2WgF1J7h4raEyxj58wLe_inCrFX8GSAHS5ffkFppkFmgSUCPTs5LcxpjWSv_mte_V7N06JxxOoJUv5Pud1y9hdtxZESlOdfd1B_VXICfy1Q3I8_82FpVSfJui4CzuCYP49JynqpFLfB01cW6zEwv4Eog3D95hVXysXypD8GZJ4oxWykkGJ-9HtsYnLf01P6EtvTPcNaOur8hADTTJdvz6vJFIi0GES24GSiGjpYgIjRkYOsVcHQPTDx_94vh0mCcsOoa4zQ6EQ/https%3A%2F%2Fhub.docker.com%2Fr%2Fbioconductor%2Fbioconductor_docker%2Ftags>) >> into Docker desktop on my Windows machine. I wanted to use the >> MultiAssayExperiment and also SummarizedExperiment, but when I tried to load >> them using the library function they were not found. Are these docker images >> preloaded with MultiAssayExperiment? Do you have any Docker images >> preloaded with MultiAssayExperiment that are well maintained and/or >> supported? >> >> I loaded the docker image from the MultiAssayExperiment's/TCGA bioconductor >> 2020 workshop and I was able to load MultiAssayExperiment using the library >> function � >> https://hub.docker.com/r/mr148/multiassayworkshop<https://secure-web.cisco.com/13jSFAuYhSC2URJ4K7zjh4ouo3I63T-6Hw8z5s-Wr2qDEf5SxOaf6kXJP4pWIKe0noQlGgA_GF6LSHHKyxFSt_LM1tgF5_GxjeTCvWXAEtKc2CjiWbaWTzsGBmRYcDqguPf6o52KE_BuYnnGxWJ9_c0WMKjztdEXwZJvZU_cQqn1moo8yPoLpvkf3LXpcDYETRkPKUo6bEpeo3dXxR4sBarXMsI3Rbm9TP30eQM9M2XzFV6-eLG_otc5kS0QZA-wNooTaDtQMDLIouLRkIF1YUHDVDdO9S4MOMaIqNVd-cOLYzpSykcoMr4an7S0DWjLiXoRdO8b1AaEz5PxkLiApiw/https%3A%2F%2Fhub.docker.com%2Fr%2Fmr148%2Fmultiassayworkshop> >> - Is this container reliable and good to use in general for working with >> SummarizedExperiment and MultiAssayExperiment in bioconductor? >> >> >> Thanks! >> >> Joe >> >> >> This email message may contain legally privileged and/or confidential >> information. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-mail and delete this email message from your computer. Thank you. >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
