[{"_1":2,"_176":-5,"_177":-5},"loaderData",{"_3":4,"_13":14,"_21":22,"_155":156},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","routes/_layout",{"_15":-5,"_16":17,"_18":17,"_19":11,"_20":11},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_23":24,"_25":-5,"_26":11,"_27":11,"_28":29,"_30":31,"_32":-5,"_33":11,"_34":35,"_84":85,"_108":109,"_146":-5,"_147":11,"_148":17,"_149":11,"_150":-5,"_151":11,"_152":-5,"_153":154},"canonicalUrl","https://hub.docker.com/r/stuartlab/monocle/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","stuartlab","reponame","monocle","cloudBuildSource","isAutobuildsAvailable","repo",{"_36":37,"_38":39,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":51,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":29,"_69":70,"_75":17,"_76":77,"_81":29,"_82":83},"categories",[],"content_types",[40],"image","date_registered","2018-08-22T20:45:59.302493Z","description","Docker container holding monocle and common format conversion code.","is_private","last_updated","2018-12-05T20:59:07.992815Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[52],"application/vnd.docker.container.image.v1+json","name","pull_count",412,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# monocle-docker\nEnvironment for executing the monocle trajectory inference algorithm.\nContains [functions](https://github.com/Stuartlab-UCSC/traj-converters) to convert the output to [common formats](https://github.com/Stuartlab-UCSC/traj-formats). The container is hosted on [docker hub](https://hub.docker.com/r/stuartlab/monocle/).\n\n\nThis readme outlines three ways the container can be used. You'll need docker installed to follow.\n\n* [Execute the container's native analysis script.](#min)\n* [Develop analysis inside container using Rstudio.](#container)\n* [Execute a user defined script inside the image.](#already)\n\n\nFor instructions below I suggest creating a shared volume,\n`./shared` in the directory you are launching the docker from. This \nvolume acts as shared storage. The shared storage is the easiest way to\naccess input and output from the container.\n\nYou can run this command in bash (R needs to be installed) to create the test expression data, exp.tab:\n\n`R -e 'set.seed(13);write.table(replicate(110, rnbinom(500, c(3, 10, 45, 100), .1)),file=\"shared/exp.tab\",col.names=1:110, sep=\"\\t\")'`\n\n## Execute the container's native analysis script:\nWe are trying to establish a convention where containers for TI algorithms have a`run_method` script in the image's $PATH. This allows a uniform interface for containers with different algorithms. The pattern is:\n\n`docker run -v $(pwd):/data run_method `\n\nIf the second positional argument is ommitted then a file called output_*method*.json will be produced. Hence, if your expression file 'exp.tab' is in your current working directory:\n\n`docker run -v $(pwd):/data stuartlab/monocle run_method exp.tab`\n\nwill produce a 'output_monocle.json' file.\n\n## Develop inside the container with Rstudio:\n\nMove into the directory you'd like to do your work in, and create a `shared` directory for the docker container.\n\n`cd some/directory && mkdir shared`\n\nLet's say you have a tab delimited expression file, `exp.tab`, you'd like to run TI analysis on. Move it into the shared directory.\n\n`cp ../../place/your/data/is/exp.tab shared`\n\nIf you don't have an exp.tab file, you may create example data with R.\n\n`R -e 'set.seed(13);write.table(replicate(110, rnbinom(500, c(3, 10, 45, 100), .1)),file=\"shared/exp.tab\",col.names=1:110, sep=\"\\t\")'`\n\nThen pull the image down (if it doesn't exist on your machine), and run an Rstudio session in your browser.\n\n`docker run -v $(pwd)/shared:/home/shared -d -p 8787:8787 -e PASSWORD=ABC123 -e ROOT=TRUE stuartlab/monocle`\n\nFrom there open your favorite browser (tested on chrome) at `http://localhost:8787/`. The password is `ABC123` and username is `rstudio`.\n\nNow you can use Rstudio to create a script that runs on your data, and save\nthe script to `/home/shared` inside the container. An example\nscript could be something like:\n\n```R\nlibrary(monocle)\nsource(\"/home/traj-converters/src/R/monocle_convert.r\")\n\nread_data <- function(){\n # Read tab matrix from shared dir.\n as.matrix(read.table(\"/home/shared/exp.tab\", sep=\"\\t\", header=T))\n}\nmonocle_analysis <- function(expression_matrix){\n # Return a completed monocle object\n cds <- newCellDataSet(expression_matrix)\n cds <- estimateSizeFactors(cds)\n cds <- estimateDispersions(cds)\n ordering_genes <- subset(dispersionTable(cds), mean_expression>=0.1)\n cds <- setOrderingFilter(cds, ordering_genes)\n cds <- reduceDimension(cds, max_components = 2, method = \"DDRTree\")\n cds <- orderCells(cds)\n return(cds)\n}\n\n# Execute pipeline.\nexp_mat <- read_data()\nmonocle_obj <- monocle_analysis(exp_mat)\n\n# Write to common format.\nwrite_common_json(monocle_obj, file=\"/home/shared/monocle.json\")\nwrite_cell_x_branch(monocle_obj, file=\"/home/shared/monocle.cxb.tab\")\n```\n\nIn reality, you'll want to toy with the monocle_analysis function and investigate the resulting monocle object with the various plot functions provided by monocle. Once you're happy with the analysis and you've saved the script in the container, say `/home/shared/my_analysis_script.r`, you can [run the script in the container](#already) to reproduce the analysis.\n\n## Execute a user defined script inside the image:\nThis command assumes that you have a script `my_analysis_script.r` in a directory named `shared` in your current working directory. To make your life easier I suggest developing this script inside the container as [above](#container). If you did not do that, it's necessary that the paths in `my_analysis_script.r` match the container's file system. This amounts to changing the paths that read and write data from `path/on/machine/*` to `/home/shared/*`. \n\nMake sure you have your data and script in a directory named `shared` so the docker has access to them.\n\n`mkdir shared && cp ../../data/for/script ./shared && cp ../../my_analysis_script ./shared`\n\nThen bind the shared directory and execute the script.\n\n`docker run -v $(pwd)/shared:/home/shared stuartlab/monocle Rscript /home/shared/my_analysis_script.r`\n\n# Working on a remote server (or behind VPN).\n\n\nFollow the steps [to develop in R studio](#container) up until you are instructed to open your favorite browser.\n\nUse an ssh tunnel to attach the localhost:8787 of the remote server to the localhost:8787 of your machine.\n\n`ssh -L 8787:localhost:8787 sammy@your_server_ip`\n\nNow you can open your favorite browser on `http://localhost:8787/` and work within the filesystem of the remote server.\n","has_starred","hub_user","immutable_tags_settings",{"_71":11,"_72":73},"enabled","rules",[74],".*","is_automated","permissions",{"_78":17,"_79":11,"_80":11},"read","write","admin","user","storage_size",9575807338,"orgData",{"_86":87,"_88":89,"_90":91,"_92":29,"_93":94,"_95":96,"_97":98,"_99":100,"_101":102,"_103":104,"_105":104,"_106":104,"_107":17},"id","5a99f3acb7424a5abcf78a999d148555","uuid","5a99f3ac-b742-4a5a-bcf7-8a999d148555","type","organization","orgname","full_name","Stuart Lab","location","Santa Cruz","company","UCSC","profile_url","https://sysbiowiki.soe.ucsc.edu/","date_joined","2016-07-14T19:08:36.117623Z","gravatar_url","","gravatar_email","badge","is_active","recentTags",[110],{"_111":40,"_112":113,"_114":115,"_86":116,"_117":118,"_46":135,"_136":113,"_137":29,"_138":52,"_53":139,"_140":141,"_142":126,"_143":135,"_144":62,"_145":17},"content_type","creator",971783,"full_size",779570724,33689935,"images",[119],{"_120":121,"_122":123,"_124":104,"_125":126,"_127":128,"_129":130,"_131":104,"_132":-5,"_133":115,"_59":62,"_134":-5},"architecture","amd64","digest","sha256:fd6242ab6261ca74a99c55212b3c34b30a71d290f1c2ba16743e978eee10dcbe","features","last_pulled","2026-09-25T02:34:25.319863009Z","last_pushed","2018-12-05T20:59:08Z","os","linux","os_features","os_version","size","variant","2018-12-05T20:59:07.478501Z","last_updater","last_updater_username","media_type","latest","repository",5922311,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_34":157,"_164":165,"_153":174,"_175":11},{"_36":158,"_38":159,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":160,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":29,"_69":161,"_75":17,"_76":163,"_81":29,"_82":83},[],[40],[52],{"_71":11,"_72":162},[74],{"_78":17,"_79":11,"_80":11},"tags",{"_166":60,"_167":-5,"_168":-5,"_169":170},"count","next","previous","results",[171],{"_111":40,"_112":113,"_114":115,"_86":116,"_117":172,"_46":135,"_136":113,"_137":29,"_138":52,"_53":139,"_140":141,"_142":126,"_143":135,"_144":62,"_145":17},[173],{"_120":121,"_122":123,"_124":104,"_125":126,"_127":128,"_129":130,"_131":104,"_132":-5,"_133":115,"_59":62,"_134":-5},[],"canDeleteTags","actionData","errors"]

stuartlab/monocle

Tags for stuartlab/monocle