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metaDataOnly <- synGet(synapseId, downloadFile=F)

activity_name <- "RNA-seq Count File Merging"
input_files <- c("syn2875347")
code_files <- list(list(name = "merge_mouse_tau_rnaseq_counts.R",
                        url = "https://github.com/jaeddy/ampSynapseProjects/blob/v0.1-alpha/dataEnablement/R/merge_mouse_tau_rnaseq_counts.R", 
                        wasExecuted = T),
                    list(name = "merge_count_files.R",
                         url = "https://github.com/jaeddy/ampSynapseProjects/blob/v0.1-alpha/dataEnablement/R/merge_count_files.R", 
                         wasExecuted = T))

bheavner

print("Hi from github :)")

print("Do you have randomForest?")

# do we want specific versions?
if(!require(randomForest, quiet = TRUE)){
  install.packages("randomForest", quiet=TRUE)
  suppressWarnings(library(randomForest))
}

bheavner

# don't commit files that may have passwords
.env
*.cnf
 
# History files
.Rhistory
.Rapp.history

# Session Data files
.RData

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return_true <- function(){
  return(TRUE)
}

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context("test_testthat - unit tests")

test_that("test_return_true returns TRUE", {
  expect_true(return_true())
})

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print("hello!")

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library(tidyverse)

parsed_snp_file <- "parsed_snp.tsv"
parsed_indel_file <- "parsed_indel.tsv"
unit_defs_file <- "feature_bounds_20170804.tsv"

snps <- read_tsv(parsed_snp_file, comment = "#")

indels <- read_tsv(parsed_indel_file, comment = "#")

bheavner

# goal: mint minids for freeze 5 annotation in exchange area.

# requires digest and minidtools libraries

# computes checksum using local copy of the file
localPath <-
  paste0("/projects/topmed/variant_annotation/freeze_5/database/v0/",
         "parsed_files/2_snv.tsv.gz")

# use location on exchange area for the location metadata in the minid

bheavner

example minid: ark:/57799/b9z705
TOMBSTONEd minid used in package: ark:/57799/b9j69h
TOPMED parsed annotation chr 2 minid: minid:b9g69w