3.2.1 Step 1: Have a plan

To demonstrate I will use a RNA-seq workflow from Bioconductor, when you open this link, you will notice a full example written in Markdown I want to make it into an app and allow you to input new files and generate new report base on this template.

Before you build any tool, you have to have a plan in mind

1. What Input, Output and Parameter you want to define for the tool
2. Is there a Docker container already available for your tool? Do you want to build one with command line interface?

First thing first, let’s define our tool first, here is a diagram generated with Seven Bridges’ graphical user interface.

• Input
  • Gene feature file
  • A list of bamfiles
  • Design matrix
• Output
  • Report in PDF, using the R Markdown associated with this workflow and example
  • Graphics
  • Differential expression table

3.2.2 Step 2: Create Docker container for your tool

Building a development environment is essential for developing your command line interface and your app. There are some principles:

1. First you need to check is there any existing container you can directly use, so you don’t have to make a new one. If you don’t know what to use, I will suggest you start with rocker/hadleyverse, it has lots of stuff like Markdown, knitr need and other Hadley’s popular packages.

Official R Docker images is called “Rocker” project and is on GitHub, please visit the page to find more details and Dockerfile.

Image	Description
rocker/r-base	base package to build from
rocker/r-devel	base + R-devel from SVN
rocker/rstudio	base + RStudio Server
rocker/hadleyverse	rstudio + Hadley’s packages, LaTeX
rocker/ropensci	hadleyverse + rOpenSci packages
rocker/r-devel-san	base, SVN’s R-devel and SAN

Bioconductor have a nice page about the official Docker images, please read for more details.

Image (release branch)	Image (development branch)
bioconductor/release_base	bioconductor/devel_base
bioconductor/release_core	bioconductor/devel_core
bioconductor/release_flow	bioconductor/devel_flow
bioconductor/release_microarray	bioconductor/devel_microarray
bioconductor/release_proteomics	bioconductor/devel_proteomics
bioconductor/release_sequencing	bioconductor/devel_sequencing
bioconductor/release_metabolomics	bioconductor/devel_metabolomics

For example, you know there is an runif function in the rocker/r-base container, you can just do something like this. Please read another tutorial called “Describe and Execute CWL Tools/Workflows in R”, it introduced a simpler example with random number generator.

rbx <- Tool(
  id = "runif",
  label = "runif",
  hints = requirements(docker(pull = "rocker/r-base"), cpu(1), mem(2000)),
  baseCommand = "Rscript -e 'runif(100)'",
  stdout = "output.txt",
  outputs = output(id = "random", glob = "*.txt")
)
rbx$toJSON(pretty = TRUE)

{
  "sbg:id": "runif",
  "id": "#runif",
  "inputs": [],
  "outputs": [
    {
      "type": ["null", "File"],
      "label": "",
      "description": "",
      "streamable": false,
      "default": "",
      "id": "#random",
      "outputBinding": {
        "glob": "*.txt"
      }
    }
  ],
  "requirements": [],
  "hints": [
    {
      "class": "DockerRequirement",
      "dockerPull": "rocker/r-base"
    },
    {
      "class": "sbg:CPURequirement",
      "value": 1
    },
    {
      "class": "sbg:MemRequirement",
      "value": 2000
    }
  ],
  "label": "runif",
  "class": "CommandLineTool",
  "baseCommand": [
    "Rscript -e 'runif(100)'"
  ],
  "arguments": [],
  "stdout": "output.txt"
} 

You can directly follow this tutorial, paste your JSON into your tool editor by click “import”. Then “save” and “run”, you will be able to run your first application on CGC with no parameters and input files.

2. If you don’t want to make a new container with command line interface and you can simply insert script temporarily for existing container. You can do things as quick as this, by provide a script in the ‘content’ of ‘fileDef’.

# provide scripts
# make a new script file
fd <- fileDef(
  name = "runif.R",
  content = "set.seed(1); runif(100)"
)
rbx <- Tool(
  id = "runif",
  label = "runif",
  hints = requirements(docker(pull = "rocker/r-base"), cpu(1), mem(2000)),
  requirements = requirements(fd),
  baseCommand = "Rscript runif.R", # run script you created.
  stdout = "output.txt",
  outputs = output(id = "random", glob = "*.txt")
)

Note: in the above example, I made a mistake on purpose, so try to debug on the platform if the task fails : )

I will introduce “Tool” function, in the later section, don’t worry.

3. For advanced developer/users: if you think a cool command line interface is worth doing, and convenient in any case, then go ahead and make one and create our own container will always be a better idea. this allow you to provide much formal interface at both command line level or container level.

Here is Dockerfile I used to generate the workflow I need

fl <- system.file("docker/rnaseqGene", "Dockerfile",
  package = "sevenbridges"
)

Here is the current content of the Dockerfile:

cat(readLines(fl), sep = "\n")

FROM rocker/tidyverse

MAINTAINER "Tengfei Yin" tengfei.yin@sevenbridges.com

RUN Rscript -e 'source("http://bioconductor.org/workflows.R"); workflowInstall("rnaseqGene")'

ADD src/performDE.R /usr/local/bin/
RUN mkdir /report
ADD report/rnaseqGene.Rmd /report/

RUN chmod a+x /usr/local/bin/performDE.R \
    && chmod -R a+x /report

It does a couple of things:

1. Install workflow I need and all dependencies
2. Insert command line interface I created, make it executable and in PATH
3. Insert full report template I am using

In the next section, I will show you how to create command line interface.

3.2.3 Step 3: Create your command line interface

In this step, I am going to:

1. Use R package docopt to make R command line interface
2. Insert my script into the container I made
3. Test function inside container

Here is the command line I am using it’s called “performDE.R”

fl <- system.file("docker/rnaseqGene/src", "performDE.R",
  package = "sevenbridges"
)

Here is the current content of the Dockerfile:

cat(readLines(fl), sep = "\n")

#!/usr/bin/Rscript
"usage: performDE.R [options]

options:
--bamfiles=<file> bamfiles
--design=<file> design data frame
--gtffile=<file> gene feature file
--format=<string> pdf or html. [default: html]
" -> doc

library("docopt")
opts <- docopt(doc)

.design <- opts$design
if (is.null(.design)) {
  .design <- system.file("extdata/sample_table.csv", package = "airway")
}

.bamfiles <- opts$bamfiles
if (is.null(.bamfiles)) {
  .bamfiles <- list.files(system.file("extdata", package = "airway"), "*.bam",
    full.names = TRUE
  )
} else {
  .bamfiles <- strsplit(opts$bamfiles, ",")[[1]]
}

.gtffile <- opts$gtffile
if (is.null(.gtffile)) {
  .gtffile <- system.file("extdata/Homo_sapiens.GRCh37.75_subset.gtf",
    package = "airway"
  )
}

# create param list
lst <- list(
  design = normalizePath(.design),
  gtffile = normalizePath(.gtffile),
  bamfiles = normalizePath(.bamfiles),
  currentPath = normalizePath(".")
)

# render the report
.format <- switch(opts$format,
  "pdf" = "pdf_document",
  "html" = "html_document", {
    "pdf_document"
  }
)

rmarkdown::render("/report/rnaseqGene.Rmd", .format,
  output_dir = ".",
  params = lst
)

# For rabix execution in the cloud,
# this is now a workaround to move intermediate files

I am using docopt package instead of commandArgs because it allows you to create a formal interface. For example, you have '--help' from command line for free. Feel free to use other methods like commandArgs() in R.

$./performDE.R --help
Loading required package: methods
usage: performDE.R [options]

options:
--bamfiles=<file> bamfiles
--design=<file> design data frame
--gtffile=<file> gene feature file
--format=<string> pdf or html. [default: html]

Sometime you want to produce a report, so in the end you will notice how I pass parameters from command line to a report.

3.2.4 Step 4: Add default report template to your app

As a developer, if you always have a fixed report template provided for you tool, you can hard-code your template into your Docker container, like you noticed in the Dockerfile I created, I insert a report R Markdown template. And in the command line interface, in the end, I pass it to rmarkdown::render function as parameters ‘param’. In this way, you define your input in the header of R Markdown. Examples like this, this template I used here, is exactly the same report on Bioconductor’s RNA-Seq workflow website.

fl <- system.file("docker/rnaseqGene/report", "rnaseqGene.Rmd",
  package = "sevenbridges"
)

Here is the current content (first 50 lines of the whole report) of the template:

cat(readLines(fl, n = 50), sep = "\n")

---
title: "Uniform random number generator example"
date: "`r Sys.Date()`"
output:
  pdf_document:
    toc: true
    toc_depth: 2
params:
  bamfiles: ""
  design: ""
  gtffile: ""
  currentPath: "."
---

# Acknowledgement

This RNA-seq test report is generated based on Biocondcutor workflow,
for experimental purpose, I tweaked the contents. Instead of a test
data, I am createing command line interface based on this document
that take new data and generate this report. It's experiments about
Docker, CWL, and Rabix.

<script type="text/javascript"
  src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>

__original documentaion comes from__

# RNA-seq workflow: gene-level exploratory analysis and differential expression

Michael Love [1], Simon Anders [2,3], Vladislav Kim [3], Wolfgang Huber [3]

[1] Department of Biostatistics, Dana-Farber Cancer Institute and
Harvard School of Public Health, Boston, US; 

[2] Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland;

[3] European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

```{r style, echo=FALSE, message=FALSE, warning=FALSE, results="asis"}
library("knitr")
library("rmarkdown")
options(width = 100)
opts_knit$set(root.dir = params$currentPath)
opts_chunk$set(message = FALSE, error = FALSE,
               warning = FALSE, fig.width = 5, fig.height = 5)
```

# Contents

See the header, you will see ‘params’ which is passed from rmarkdown::render, so you can use it directly in the report like params$bamfiles.

Now you have

• Dockerfile
• Command line interface with report template

You are ready to build Docker container and push it to the registry. You can choose to use registry like dockerhub or use CGC’s own Docker registry (cgc-images.sbgenomics.com). To learn how to use CGC Image registry, please read out tutorial.

3.2.5 Step 5: Describe your tool in R into CWL

Finally it’s time to describe your tool in R (CWL format)!

Well, you are always encouraged to use graphical user interface, but it is at the same time fun to learn how to do it in R, so you could script how you build it together, like what I did here, for every single tool JSON, I have an R script called generator.R in the same folder, so I can always trace back.

For example, you can see the same in the sbg/sevenbridges-r GitHub repo, under inst/docker, you will see three examples, 1. package Docker 2. RNA-Seq tool 3. report tool, under each folder, you will see 1. one Dockerfile, 2. src/ for command line 3. report/ for report template and 4. rabix a generator file and a JSON.

Tool is the simple basic unit of a workflow, you can put the whole flow in one container and one tool, it of course works, just make it hard to factorize components. This is the exact example, I can make one tool for DESeq2 and one tool for Rsamtools, I can also put everything I need in one tool and provide single functionality.

Note: you can use single Docker image, but describe as many tools as you want if it contains what you need such as different command.

Follow the example to create Tool with Tool function. It’s straightforward. Especially if you are familiar with Seven Bridges Tool editor already.

Hints: please pay attention to how I create

• File list: via ItemArray(“File”) or “File…” this allow you to input multiple files form the task page.
• Single File: just “File”, only single file allowed.
• Expression to specify the javascript expression (note:it’s convenient to do it with graphic user interface, because you can directly see the result of the expression)
• Enum: call ‘enum’.

rbx <- Tool(
  id = "rnaseqGene",
  label = "rnaseqgene",
  description = "A RNA-seq Differiencial Expression Flow and Report",
  hints = requirements(docker(pull = "tengfei/rnaseqgene"), cpu(1), mem(2000)),
  baseCommand = "performDE.R",
  inputs = list(
    input(
      id = "bamfiles", label = "bam files",
      description = "a list of bam files",
      type = "File...", ## or type = ItemArray("File")
      prefix = "--bamfiles",
      itemSeparator = ","
    ),
    input(
      id = "design", label = "design matrix",
      type = "File",
      prefix = "--design"
    ),
    input(
      id = "gtffile", label = "gene feature files",
      type = "File",
      prefix = "--gtffile"
    ),
    input(
      id = "format", label = "report foramt html or pdf",
      type = enum("format", c("pdf", "html")),
      prefix = "--format"
    )
  ),
  outputs = list(
    output(
      id = "report", label = "report",
      description = "A reproducible report created by Rmarkdown",
      glob = Expression(
        engine = "#cwl-js-engine",
        script = "x = $job[['inputs']][['format']]; if(x == 'undefined' || x == null){x = 'html';};'rnaseqGene.' +  x"
      )
    ),
    output(
      id = "heatmap", label = "heatmap",
      description = "A heatmap plot to show the Euclidean distance between samples",
      glob = "heatmap.pdf"
    ),
    output(
      id = "count", label = "count",
      description = "Reads counts matrix",
      glob = "count.csv"
    ),
    output(
      id = "de", label = "Differential expression table",
      description = "Differential expression table",
      glob = "de.csv"
    )
  )
)

By default it output YAML, but you can print it into JSON as well.

rbx

sbg:id: rnaseqGene
id: '#rnaseqGene'
inputs:
- type:
  - 'null'
  - items: File
    type: array
  label: bam files
  description: a list of bam files
  streamable: no
  default: ''
  id: '#bamfiles'
  inputBinding:
    position: 0
    prefix: --bamfiles
    separate: yes
    itemSeparator: ','
    shellQuote: no
    sbg:cmdInclude: yes
    streamable: no
    separator: ' '
  required: no
- type:
  - 'null'
  - File
  label: design matrix
  description: ''
  streamable: no
  default: ''
  id: '#design'
  inputBinding:
    position: 0
    prefix: --design
    separate: yes
    shellQuote: no
    sbg:cmdInclude: yes
    streamable: no
    separator: ' '
  required: no
- type:
  - 'null'
  - File
  label: gene feature files
  description: ''
  streamable: no
  default: ''
  id: '#gtffile'
  inputBinding:
    position: 0
    prefix: --gtffile
    separate: yes
    shellQuote: no
    sbg:cmdInclude: yes
    streamable: no
    separator: ' '
  required: no
- type:
  - 'null'
  - name: format
    symbols:
    - pdf
    - html
    type: enum
  label: report foramt html or pdf
  description: ''
  streamable: no
  default: ''
  id: '#format'
  inputBinding:
    position: 0
    prefix: --format
    separate: yes
    shellQuote: no
    sbg:cmdInclude: yes
    streamable: no
    separator: ' '
  required: no
outputs:
- type:
  - 'null'
  - File
  label: report
  description: A reproducible report created by Rmarkdown
  streamable: no
  default: ''
  id: '#report'
  outputBinding:
    glob:
      engine: '#cwl-js-engine'
      script: x = $job[['inputs']][['format']]; if(x == 'undefined' || x == null){x
        = 'html';};'rnaseqGene.' +  x
      class: Expression
- type:
  - 'null'
  - File
  label: heatmap
  description: A heatmap plot to show the Euclidean distance between samples
  streamable: no
  default: ''
  id: '#heatmap'
  outputBinding:
    glob: heatmap.pdf
- type:
  - 'null'
  - File
  label: count
  description: Reads counts matrix
  streamable: no
  default: ''
  id: '#count'
  outputBinding:
    glob: count.csv
- type:
  - 'null'
  - File
  label: Differential expression table
  description: Differential expression table
  streamable: no
  default: ''
  id: '#de'
  outputBinding:
    glob: de.csv
requirements: []
hints:
- class: DockerRequirement
  dockerPull: tengfei/rnaseqgene
- class: sbg:CPURequirement
  value: 1
- class: sbg:MemRequirement
  value: 2000
label: rnaseqgene
description: A RNA-seq Differiencial Expression Flow and Report
class: CommandLineTool
baseCommand:
- performDE.R
arguments: []

rbx$toJSON(pretty = TRUE)

{
  "sbg:id": "rnaseqGene",
  "id": "#rnaseqGene",
  "inputs": [
    {
      "type": [
        "null",
        {
          "items": "File",
          "type": "array"
        }
      ],
      "label": "bam files",
      "description": "a list of bam files",
      "streamable": false,
      "default": "",
      "id": "#bamfiles",
      "inputBinding": {
        "position": 0,
        "prefix": "--bamfiles",
        "separate": true,
        "itemSeparator": ",",
        "shellQuote": false,
        "sbg:cmdInclude": true,
        "streamable": false,
        "separator": " "
      },
      "required": false
    },
    {
      "type": ["null", "File"],
      "label": "design matrix",
      "description": "",
      "streamable": false,
      "default": "",
      "id": "#design",
      "inputBinding": {
        "position": 0,
        "prefix": "--design",
        "separate": true,
        "shellQuote": false,
        "sbg:cmdInclude": true,
        "streamable": false,
        "separator": " "
      },
      "required": false
    },
    {
      "type": ["null", "File"],
      "label": "gene feature files",
      "description": "",
      "streamable": false,
      "default": "",
      "id": "#gtffile",
      "inputBinding": {
        "position": 0,
        "prefix": "--gtffile",
        "separate": true,
        "shellQuote": false,
        "sbg:cmdInclude": true,
        "streamable": false,
        "separator": " "
      },
      "required": false
    },
    {
      "type": [
        "null",
        {
          "name": "format",
          "symbols": ["pdf", "html"],
          "type": "enum"
        }
      ],
      "label": "report foramt html or pdf",
      "description": "",
      "streamable": false,
      "default": "",
      "id": "#format",
      "inputBinding": {
        "position": 0,
        "prefix": "--format",
        "separate": true,
        "shellQuote": false,
        "sbg:cmdInclude": true,
        "streamable": false,
        "separator": " "
      },
      "required": false
    }
  ],
  "outputs": [
    {
      "type": ["null", "File"],
      "label": "report",
      "description": "A reproducible report created by Rmarkdown",
      "streamable": false,
      "default": "",
      "id": "#report",
      "outputBinding": {
        "glob": {
          "engine": "#cwl-js-engine",
          "script": "x = $job[['inputs']][['format']]; if(x == 'undefined' || x == null){x = 'html';};'rnaseqGene.' +  x",
          "class": "Expression"
        }
      }
    },
    {
      "type": ["null", "File"],
      "label": "heatmap",
      "description": "A heatmap plot to show the Euclidean distance between samples",
      "streamable": false,
      "default": "",
      "id": "#heatmap",
      "outputBinding": {
        "glob": "heatmap.pdf"
      }
    },
    {
      "type": ["null", "File"],
      "label": "count",
      "description": "Reads counts matrix",
      "streamable": false,
      "default": "",
      "id": "#count",
      "outputBinding": {
        "glob": "count.csv"
      }
    },
    {
      "type": ["null", "File"],
      "label": "Differential expression table",
      "description": "Differential expression table",
      "streamable": false,
      "default": "",
      "id": "#de",
      "outputBinding": {
        "glob": "de.csv"
      }
    }
  ],
  "requirements": [],
  "hints": [
    {
      "class": "DockerRequirement",
      "dockerPull": "tengfei/rnaseqgene"
    },
    {
      "class": "sbg:CPURequirement",
      "value": 1
    },
    {
      "class": "sbg:MemRequirement",
      "value": 2000
    }
  ],
  "label": "rnaseqgene",
  "description": "A RNA-seq Differiencial Expression Flow and Report",
  "class": "CommandLineTool",
  "baseCommand": [
    "performDE.R"
  ],
  "arguments": []
} 

rbx$toJSON()

{"sbg:id":"rnaseqGene","id":"#rnaseqGene","inputs":[{"type":["null",{"items":"File","type":"array"}],"label":"bam files","description":"a list of bam files","streamable":false,"default":"","id":"#bamfiles","inputBinding":{"position":0,"prefix":"--bamfiles","separate":true,"itemSeparator":",","shellQuote":false,"sbg:cmdInclude":true,"streamable":false,"separator":" "},"required":false},{"type":["null","File"],"label":"design matrix","description":"","streamable":false,"default":"","id":"#design","inputBinding":{"position":0,"prefix":"--design","separate":true,"shellQuote":false,"sbg:cmdInclude":true,"streamable":false,"separator":" "},"required":false},{"type":["null","File"],"label":"gene feature files","description":"","streamable":false,"default":"","id":"#gtffile","inputBinding":{"position":0,"prefix":"--gtffile","separate":true,"shellQuote":false,"sbg:cmdInclude":true,"streamable":false,"separator":" "},"required":false},{"type":["null",{"name":"format","symbols":["pdf","html"],"type":"enum"}],"label":"report foramt html or pdf","description":"","streamable":false,"default":"","id":"#format","inputBinding":{"position":0,"prefix":"--format","separate":true,"shellQuote":false,"sbg:cmdInclude":true,"streamable":false,"separator":" "},"required":false}],"outputs":[{"type":["null","File"],"label":"report","description":"A reproducible report created by Rmarkdown","streamable":false,"default":"","id":"#report","outputBinding":{"glob":{"engine":"#cwl-js-engine","script":"x = $job[['inputs']][['format']]; if(x == 'undefined' || x == null){x = 'html';};'rnaseqGene.' +  x","class":"Expression"}}},{"type":["null","File"],"label":"heatmap","description":"A heatmap plot to show the Euclidean distance between samples","streamable":false,"default":"","id":"#heatmap","outputBinding":{"glob":"heatmap.pdf"}},{"type":["null","File"],"label":"count","description":"Reads counts matrix","streamable":false,"default":"","id":"#count","outputBinding":{"glob":"count.csv"}},{"type":["null","File"],"label":"Differential expression table","description":"Differential expression table","streamable":false,"default":"","id":"#de","outputBinding":{"glob":"de.csv"}}],"requirements":[],"hints":[{"class":"DockerRequirement","dockerPull":"tengfei/rnaseqgene"},{"class":"sbg:CPURequirement","value":1},{"class":"sbg:MemRequirement","value":2000}],"label":"rnaseqgene","description":"A RNA-seq Differiencial Expression Flow and Report","class":"CommandLineTool","baseCommand":["performDE.R"],"arguments":[]} 

# # or write to an external file
# fl <- "~/Downloads/rnaseqGene.json"
# write(rbx$toJSON(pretty = TRUE), fl)

Now you want to add app to your project p, by calling app_add method, the first argument is name, the second is either a CWL JSON file, Tool object, or Workflow object.

# add App you just created
(rna.app <- p$app_add("rnaseqgene", rbx))

Please go check your app in your project, check input output and how it maps to the UI.

3.2.6 Step 6: Execute your tool with a new task via R API

Now let’s create a task and execute it with example files. You need to pass unique file id as input, so the first thing is to get file id you need for that project.

Now let’s import some files to your project for this tutorial, you can also do it via our API client by call upload function on project object. It supports

• Single file, multiple file, and folder (recursively all files) as first arugment
• name: a new name (with single file upload)
• overwrite = TRUE to overwrite existing file
• metadata: a list of meta otherwise search for the same file name ended with “.meta”

For example:

fl <- system.file("extdata", "sample1.fastq", package = "sevenbridges")
(p <- a$project(id = "tengfei/quickstart"))
# by default load .meta for the file
p$upload(fl, overwrite = TRUE)
# pass metadata
p$upload(fl, overwrite = TRUE, metadata = list(library_id = "testid2", platform = "Illumina x11"))
# rename
p$upload(fl,
  overwrite = TRUE, name = "sample_new_name.fastq",
  metadata = list(library_id = "new_id")
)

# upload folder
dir.ext <- system.file("extdata", package = "sevenbridges")
p$upload(dir.ext, overwrite = TRUE)

# upload file list
fls <- list.files(dir.ext, recursive = TRUE, full.names = TRUE)
p$upload(fls, overwrite = TRUE)

For now try using our graphic user interface to import all files listed here:

download.fl <- system.file("extdata/download.txt", package = "sevenbridges")
cat(readLines(download.fl), sep = "\n")

Warning in readLines(download.fl): incomplete final line found on '/tmp/
Rtmpc3LjJw/Rinst7ca014d2e467/sevenbridges/extdata/download.txt'

https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/example_report.Rmd
https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/hello-markdown.Rmd
https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/hello.tar
https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/Homo_sapiens.GRCh37.75_subset.gtf
https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/sample_table.csv
https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/scatter_plot.tar
https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/SRR1039508_subset.bam
https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/SRR1039509_subset.bam
https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/SRR1039512_subset.bam
https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/SRR1039513_subset.bam
https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/SRR1039516_subset.bam
https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/SRR1039517_subset.bam
https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/SRR1039520_subset.bam
https://raw.githubusercontent.com/tengfei/resource/master/2016/04-01-hackathon/data/SRR1039521_subset.bam

To use the API to uplaod, let’s download it to a folder and upload via API.

td <- tempfile()
dir.create(td)
for (f in readLines(download.fl)) {
  download.file(f, file.path(td, basename(f)))
}
# double check
list.files(td)
# upload to the project you created
p$upload(td)

Copy this list, and then in your project, click “add files”, and choose “import from ftp” (tutorial).

When it’s finished, refresh your file page, you will be able to see all of them. The cool thing is that you can search file by ‘name’ not by id, it support fuzzy pattern match.

# get file id you need as inout
(bamfiles.in <- p$file(".bam"))
(design.in <- p$file("sample_table.csv"))
(gtf.in <- p$file("Homo_sapiens.GRCh37.75_subset.gtf"))

Note: you can also passed a list of files like this, to give exact file names

bam1 <- p$file("SRR1039516_subset.bam")
bam2 <- p$file("SRR1039512_subset.bam")
bamfiles.in2 <- list(bam1, bam2)

Now create a new draft task in your project, don’t forget to pass input.

# add a new Task
(tsk <- p$task_add(
  name = "RNA DE report new",
  description = "RNA DE analysis report",
  app = rna.app$id,
  inputs = list(
    bamfiles = bamfiles.in,
    design = design.in,
    gtffile = gtf.in
  )
))

# don't forget to run a draft task
tsk$run()

To monitor the task, run following command, it will tell you when it’s finished, but this is not running in the background now.

# # monitor the task
# tsk$monitor()

A better way is to use the Task hook function, it’s flexible, you can hook any function to a task status. For example, when it’s complete download the files. Now try to send your self a text message : )

setTaskHook("completed", function() {
  tsk$download("~/Downloads")
})
tsk$monitor()

To download all files from a completed tasks

tsk$download("~/Downloads")

To run task in batch mode, check ?batch for more details. Here is an mock running:

# batch by items
(tsk <- p$task_add(
  name = "RNA DE report new batch 2",
  description = "RNA DE analysis report",
  app = rna.app$id,
  batch = batch(input = "bamfiles"),
  inputs = list(
    bamfiles = bamfiles.in,
    design = design.in,
    gtffile = gtf.in
  )
))

# batch by metadata, input files has to have metadata fields specified
(tsk <- p$task_add(
  name = "RNA DE report new batch 3",
  description = "RNA DE analysis report",
  app = rna.app$id,
  batch = batch(
    input = "fastq",
    c("metadata.sample_id", "metadata.library_id")
  ),
  inputs = list(
    bamfiles = bamfiles.in,
    design = design.in,
    gtffile = gtf.in
  )
))

For more details, check R API tutorial.

3.3.1 What is report tool?

In our last section, we demonstrate how to hardcode a R report template into your Docker container and your command line will output a new report with new input files.

But how about this, instead of coding template into Docker, I want to

• Provide multiple R markdown template as input
• Provide multiple shiny template as input
• Provide multiple liftr template as input
• Collect files from a flow used for my report
• Collect report from different tools of a single workflow and compile a summary report

Here I am developing a report tool to support all these in a single tool and it uses two different engines to provide isolated environment to generate report, because each report has different dependencies.

• packrat engine: isolated libraries
• liftr engine (in progress): Docker in Docker

Requirement for your report template

This is how it works

1. An app folder is created for each template
2. In this root folder, you have data, src, www folders, on the interface, you can connect output into those folders, so data flows into it.
3. First copy what’s in your template, then copy those task output into those folders.
4. Now create isolated environment by packrat or liftr.
5. Compile your template into report or new Shiny app
6. If you pass shinyapp.io token, name, secret, will deploy shiny app for you!
7. So in your template, you have to know file name and location relative to your app root, this is the most important requirement now.

If you are interested, you can still read my Dockerfile, command line, tool generator and JSON.

I will suggest you directly copy the json into your project. Just to try add an app in a different way.

fl <- system.file("docker/reporttool/rabix/reporttool.json",
  package = "sevenbridges"
)
cat(readLines(fl), sep = "\n")

{
  "sbg:id": "reporttool",
  "id": "#reporttool",
  "inputs": [
    {
      "type": [
        "null",
        {
          "items": "File",
          "type": "array"
        }
      ],
      "label": "",
      "description": "Shinay app template as zipped(.zip) or tar(tar.gz) file.",
      "streamable": false,
      "default": "",
      "id": "#shinyTemplate",
      "inputBinding": {
        "position": 0,
        "prefix": "--shinyTemplate",
        "separate": true,
        "itemSeparator": ",",
        "sbg:cmdInclude": true
      }
    },
    {
      "type": [
        "null",
        {
          "items": "File",
          "type": "array"
        }
      ],
      "label": "",
      "description": "Rmarkdown file template will be rendered by knitr",
      "streamable": false,
      "default": "",
      "id": "#knitrTemplate",
      "inputBinding": {
        "position": 0,
        "prefix": "--knitrTemplate",
        "separate": true,
        "itemSeparator": ",",
        "sbg:cmdInclude": true
      }
    },
    {
      "type": [
        "null",
        {
          "items": "File",
          "type": "array"
        }
      ],
      "label": "",
      "description": "Files to be included in data folder of app",
      "streamable": false,
      "default": "",
      "id": "#data",
      "inputBinding": {
        "position": 0,
        "prefix": "--data",
        "separate": true,
        "itemSeparator": ",",
        "sbg:cmdInclude": true
      }
    },
    {
      "type": [
        "null",
        {
          "items": "File",
          "type": "array"
        }
      ],
      "label": "",
      "description": "Files to be included in www folder of app",
      "streamable": false,
      "default": "",
      "id": "#www",
      "inputBinding": {
        "position": 0,
        "prefix": "--www",
        "separate": true,
        "itemSeparator": ",",
        "sbg:cmdInclude": true
      }
    },
    {
      "type": [
        "null",
        {
          "items": "File",
          "type": "array"
        }
      ],
      "label": "",
      "description": "Files to be included in src folder of app",
      "streamable": false,
      "default": "",
      "id": "#src",
      "inputBinding": {
        "position": 0,
        "prefix": "--src",
        "separate": true,
        "sbg:cmdInclude": true
      }
    },
    {
      "type": [
        "null",
        {
          "items": "File",
          "type": "array"
        }
      ],
      "label": "",
      "description": "Files to be included in root of app folder",
      "streamable": false,
      "default": "",
      "id": "#appFiles",
      "inputBinding": {
        "position": 0,
        "prefix": "--appFiles",
        "separate": true,
        "itemSeparator": ",",
        "sbg:cmdInclude": true
      }
    },
    {
      "type": ["null", "string"],
      "label": "",
      "description": "Name of account to save or remove, check shinyapps::setAccountInfo",
      "streamable": false,
      "default": "",
      "id": "#name",
      "inputBinding": {
        "position": 0,
        "prefix": "--name",
        "separate": true,
        "sbg:cmdInclude": true
      }
    },
    {
      "type": ["null", "string"],
      "label": "",
      "description": "User token for the account, check shinyapps::setAccountInfo",
      "streamable": false,
      "default": "",
      "id": "#token",
      "inputBinding": {
        "position": 0,
        "prefix": "--token",
        "separate": true,
        "sbg:cmdInclude": true
      }
    },
    {
      "type": ["null", "string"],
      "label": "",
      "description": "User secret for the account, check shinyapps::setAccountInfo",
      "streamable": false,
      "default": "",
      "id": "#secret",
      "inputBinding": {
        "position": 0,
        "prefix": "--secret",
        "separate": true,
        "sbg:cmdInclude": true
      }
    },
    {
      "type": ["null", "string"],
      "label": "",
      "description": "Optional; the kind of content being deployed (e.g. 'plot', 'document', or 'application').",
      "streamable": false,
      "default": "",
      "id": "#contentCategory",
      "inputBinding": {
        "position": 0,
        "prefix": "--contentCategory",
        "separate": true,
        "sbg:cmdInclude": true
      }
    },
    {
      "type": ["null", "string"],
      "label": "",
      "description": "Account to deploy application to. This parameter is only required for the initial deployment of an application when there are multiple accounts configured on the system (see accounts).",
      "streamable": false,
      "default": "",
      "id": "#account",
      "inputBinding": {
        "position": 0,
        "prefix": "--account",
        "separate": true,
        "sbg:cmdInclude": true
      }
    },
    {
      "type": ["null", "string"],
      "label": "",
      "description": "Server name. Required only if you use the same account name on multiple servers.",
      "streamable": false,
      "default": "",
      "id": "#server",
      "inputBinding": {
        "position": 0,
        "prefix": "--server",
        "separate": true,
        "sbg:cmdInclude": true
      }
    },
    {
      "type": ["null", "boolean"],
      "label": "",
      "description": "Request that no status information be printed to the console during the deployment.",
      "streamable": false,
      "default": "",
      "id": "#quiet",
      "inputBinding": {
        "position": 0,
        "prefix": "--quiet",
        "separate": true,
        "sbg:cmdInclude": true
      }
    },
    {
      "type": [
        "null",
        {
          "name": "engine",
          "symbols": ["packrat", "liftr"],
          "type": "enum"
        }
      ],
      "label": "",
      "description": "packrat or liftr (docker in docker) or NA [default: packrat]",
      "streamable": false,
      "default": "",
      "id": "#engine",
      "inputBinding": {
        "position": 0,
        "prefix": "--engine",
        "separate": true,
        "sbg:cmdInclude": true
      }
    }
  ],
  "outputs": [
    {
      "type": [
        "null",
        {
          "items": "File",
          "type": "array"
        }
      ],
      "label": "",
      "description": "compressed shiny app folder",
      "streamable": false,
      "default": "",
      "id": "#shinyapp",
      "outputBinding": {
        "glob": "*.tar"
      }
    },
    {
      "type": [
        "null",
        {
          "items": "File",
          "type": "array"
        }
      ],
      "label": "",
      "description": "report rendered as html from knitr template",
      "streamable": false,
      "default": "",
      "id": "#html_report",
      "outputBinding": {
        "glob": "*.html"
      }
    },
    {
      "type": [
        "null",
        {
          "items": "File",
          "type": "array"
        }
      ],
      "label": "",
      "description": "report rendered as pdf from knitr template",
      "streamable": false,
      "default": "",
      "id": "#pdf_report",
      "outputBinding": {
        "glob": "*.pdf"
      }
    }
  ],
  "requirements": [],
  "hints": [
    {
      "class": "DockerRequirement",
      "dockerPull": "tengfei/reporttool",
      "dockerLoad": "",
      "dockerFile": "",
      "dockerImageId": "",
      "dockerOutputDirectory": ""
    }
  ],
  "label": "reporttool",
  "description": "Reporiting tools support you pass shiny app and knitr Rmakrdown template",
  "class": "CommandLineTool",
  "baseCommand": [
    "report.R"
  ],
  "arguments": [],
  "context": ""
}

Or just use API to add the raw JSON file

# directly add json file
p <- a$project(id = "tengfei/hackathon")
(report.app <- p$app_add("report-tool", fl))

Checkout the Dockerfile

fl <- system.file("docker/reporttool/Dockerfile",
  package = "sevenbridges"
)
cat(readLines(fl), sep = "\n")

FROM rocker/tidyverse

MAINTAINER "Tengfei Yin" tengfei.yin@sevenbridges.com

RUN rm -f /var/lib/dpkg/available \
    && rm -rf  /var/cache/apt/* \
    && apt-get update \
    && apt-get install -y libssl-dev

RUN R -e "install.packages(c('packrat', 'devtools', 'rsconnect', 'shiny', 'rmarkdown'), repos = 'https://cloud.r-project.org/')"

ADD src/report.R /usr/local/bin/

RUN chmod a+x /usr/local/bin/report.R

Checkout the command line

fl <- system.file("docker/reporttool/src/report.R",
  package = "sevenbriges"
)
cat(readLines(fl), sep = "\n")

Checkout the tool generator

fl <- system.file("docker/reporttool/rabix/generator.R",
  package = "sevenbriges"
)
cat(readLines(fl), sep = "\n")