dynwrapv2

.travis.yml

@@ -1,31 +1,36 @@
 language: r
 dist: trusty
-bioc_required: true
 sudo: true
 os:
- - linux
+- linux
 cache:
  directories:
-  - $HOME/.cache # hdf5, singularity
-  - $HOME/R/Library
+ - "$HOME/.cache"
+ - "$HOME/R/Library"
 services:
- - docker
-env:
- - CONTAINER=docker
- - CONTAINER=singularity
-addons:
- apt:
- packages:
- - libssh-dev # PRISM > ssh > libssh-dev
+- docker
 before_install:
- - git clone https://github.com/dynverse/travis_scripts.git
- - source travis_scripts/hdf5.sh
- - if [ "$CONTAINER" == "singularity" ]; then source travis_scripts/singularity.sh; fi
+- openssl aes-256-cbc -K $encrypted_d8a2d8b1d6fc_key -iv $encrypted_d8a2d8b1d6fc_iv
+ -in credentials.enc -out credentials -d
+- source credentials
+- source <(curl -sSL https://raw.githubusercontent.com/dynverse/travis_scripts/master/helper.sh)
 install:
- - R -e 'if ("devtools" %in% rownames(installed.packages())) update.packages(oldPkgs = "devtools", ask = FALSE) else install.packages("devtools")'
- - R -e 'devtools::install_github("dynverse/dynwrap", dep = TRUE, upgrade = TRUE)'
- - R -e 'devtools::install_github("dynverse/dyntoy", upgrade = TRUE)'
- - R -e 'devtools::install_github("dynverse/dyneval", dep = TRUE, upgrade = TRUE)'
+- set -e
+- update_docker
+- install_hdf5
+- install_cran remotes
+- install_github_withdeps dynverse/dynwrap@singularity3 dynverse/dyntoy
 script:
- - if [ "$CONTAINER" == "singularity" ]; then source travis_scripts/test_singularity_image.sh; fi
- - if [ "$CONTAINER" == "docker" ]; then source travis_scripts/test_docker_image.sh; fi
+- source version
+- build_docker
+- test_docker
+after_success:
+- push_docker
+jobs:
+ include:
+ - stage: cache
+ script:
+ - echo Do not build or test docker since this is a cache warmup
+ after_success:
+ - echo Do not push docker since this is a cache warmup
+ - stage: build

Dockerfile

@@ -1,9 +1,9 @@
-FROM dynverse/dynwrap:r
+FROM dynverse/dynwrapr:v0.1.0
 
-RUN R -e 'devtools::install_cran("SLICER")'
+ARG GITHUB_PAT
 
-LABEL version 0.1.6
+RUN R -e 'devtools::install_cran("SLICER")'
 
-ADD . /code
+COPY definition.yml run.R example.h5 /code/
 
-ENTRYPOINT Rscript /code/run.R
+ENTRYPOINT ["/code/run.R"]

definition.yml

@@ -1,62 +1,68 @@
-id: slicer
-docker_repository: dynverse/ti_slicer
-singularity_collection: 1581
-container_url: https://github.com/dynverse/ti_slicer
-name: SLICER
-source: tool
-platform: R
-doi: 10.1186/s13059-016-0975-3
-google_scholar_cluster_id: '2071780199208319199'
-trajectory_types:
-- cycle
-- linear
-- bifurcation
-- convergence
-- multifurcation
-- binary_tree
-- tree
-- acyclic_graph
-- graph
-topology_inference: free
-license: GPL-2
-preprint_date: '2016-04-09'
-publication_date: '2016-05-23'
-code_url: https://github.com/jw156605/SLICER
+method:
+ id: slicer
+ name: SLICER
+ tool_id: slicer
+ source: tool
+ platform: R
+ url: https://github.com/jw156605/SLICER
+ license: GPL-2
+ authors:
+ - given: Joshua
+ family: Welch
+ email: [email protected]
+ github: jw156605
+ - given: Jan
+ family: Prins
+ email: [email protected]
+
+
+manuscript:
+ doi: 10.1186/s13059-016-0975-3
+ google_scholar_cluster_id: '2071780199208319199'
+ preprint_date: '2016-04-09'
+ publication_date: '2016-05-23'
+
+container:
+ url: https://github.com/dynverse/ti_slicer
+ docker: dynverse/ti_slicer
+
+wrapper:
+ type: cell_graph
+ topology_inference: free
+ trajectory_types:
+ - cycle
+ - linear
+ - bifurcation
+ - convergence
+ - multifurcation
+ - binary_tree
+ - tree
+ - acyclic_graph
+ - graph
+ example: /code/example.R
+ input_required:
+ - expression
+ - start_id
+ input_optional:
+ - features_id
+ - end_id
+
 parameters:
- kmin:
+ - id: kmin
  type: integer
  default: 10
- upper: 20
- lower: 2
+ distribution:
+ type: uniform
+ upper: 20
+ lower: 2
  description: Smallest value of k to try
- m:
+ - id: m
  type: integer
  default: 2
- upper: 20
- lower: 2
+ distribution:
+ type: uniform
+ upper: 20
+ lower: 2
  description: 'Intrinsic dimension of the data. This parameter mainly influences
  the visualisation of the results. The real intrinsic dimension will be calculated
  automaticly. '
-input:
- format: rds
- optional:
- - features_id
- - end_id
- required:
- - expression
- - start_id
-output:
- format: rds
- outputs:
- - cell_graph
- - timings
- - dimred
-wrapper_type: cell_graph
-authors:
-- given: Joshua
- family: Welch
- email: [email protected]
- github: jw156605
-- given: Jan
- family: Prins
- email: [email protected]

example.R

@@ -1,8 +1,19 @@
+#!/usr/local/bin/Rscript
+
+# generate dataset with certain seed
 set.seed(1)
 data <- dyntoy::generate_dataset(
  id = "specific_example/slicer",
- num_cells = 99,
  num_features = 101,
- model = "tree"
+ model = "tree",
+ normalise = FALSE
 )
-params <- list()
+
+# add method specific args (if needed)
+data$params <- list()
+
+data$seed <- 1
+
+# write example dataset to file
+file <- commandArgs(trailingOnly = TRUE)[[1]]
+dynutils::write_h5(data, file)

run.R

@@ -1,3 +1,7 @@
+#!/usr/local/bin/Rscript
+
+task <- dyncli::main()
+
 library(jsonlite)
 library(readr)
 library(dplyr)
@@ -10,20 +14,11 @@ library(igraph)
 # ____________________________________________________________________________
 # Load data ####
 
-data <- read_rds("/ti/input/data.rds")
-params <- jsonlite::read_json("/ti/input/params.json")
-
-
-#' @examples
-#' data <- dyntoy::generate_dataset(id = "test", num_cells = 300, num_features = 300, model = "linear") %>% c(., .$prior_information)
-#' params <- yaml::read_yaml("containers/slicer/definition.yml")$parameters %>%
-#' {.[names(.) != "forbidden"]} %>%
-#' map(~ .$default)
-
-expression <- data$expression
-start_id <- data$start_id
-features_id <- data$features_id
-end_id <- data$end_id
+expression <- as.matrix(task$expression)
+params <- task$params
+start_id <- task$priors$start_id
+features_id <- task$priors$features_id
+end_id <- task$priors$end_id
 
 start_cell <- sample(start_id, 1)
 
@@ -81,16 +76,12 @@ nodes_to_keep <- unique(sh_p_to_ends$vpath %>% unlist)
 cell_ids <- names(igraph::V(traj_graph))
 to_keep <- setNames(seq_along(cell_ids) %in% nodes_to_keep, cell_ids)
 
-# return output
-output <- lst(
- cell_ids,
- cell_graph,
- to_keep,
- dimred = traj_lle,
- timings = checkpoints
-)
-
 # ____________________________________________________________________________
 # Save output ####
 
-write_rds(output, "/ti/output/output.rds")
+output <- dynwrap::wrap_data(cell_ids = cell_ids) %>%
+ dynwrap::add_cell_graph(cell_graph = cell_graph, to_keep = to_keep) %>%
+ dynwrap::add_dimred(dimred = traj_lle) %>%
+ dynwrap::add_timings(timings = checkpoints)
+
+output %>% dyncli::write_output(task$output)

version

@@ -0,0 +1 @@
+VERSION=0.9.9