@@ -1,6 +1,6 @@

 Package: ReUseData

 Title: Reusable and reproducible Data Management

-Version: 0.99.37

+Version: 0.99.38

 Authors@R: 

     person(given = "Qian",

            family = "Liu",

@@ -48,12 +48,17 @@ STAR_index <- addMeta(

         date = Sys.Date(),

         url = "https://github.com/alexdobin/STAR",

         example = paste(

-            "recipeLoad('STAR_index.R', return = TRUE)",

+            "STAR_index <- recipeLoad('STAR_index.R')",

             "STAR_index$ref <- 'gcpData/reference_genome/GRCh38.primary_assembly.genome.fa'",

             "STAR_index$gtf <- 'gcpData/gencode_annotation/gencode.v42.annotation.gtf'",

             "STAR_index$sjdb <- 100",

             "STAR_index$genomeDir <- 'GRCh38.GENCODE.v42_100'",

             "STAR_index$threads <- 16",

             "getData(STAR_index, outdir = 'gcpData', notes =c('STAR_index', 'GRCh38.primary_assembly', 'gencode.v42', 'star_2.7.9a'))",

+            "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('STAR_index', 'GRCh38.primary_assembly', 'gencode.v42', 'star_2.7.9a'))",

+            "", 

             sep="\n"))

 )

@@ -25,8 +25,13 @@ bowtie2_index <- addMeta(

         date = Sys.Date(),

         url = "https://bowtie-bio.sourceforge.net/bowtie2/index.shtml",

         example = paste(

-            "recipeLoad('bowtie2_index.R', return = TRUE)",

-            "bowtie2_index$genome <- 'GRCh38.primary_assembly.genome.fa'",

+            "bowtie2_index <- recipeLoad('bowtie2_index')",

+            "bowtie2_index$genome <- 'GRCh38.primary_assembly.genome.fa' ## need to be a valid file path", 

             "getData(bowtie2_index, outdir = 'data/folder', notes = c('bowtie2_index', 'GRCh38.primary_assembly'))",

+            "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('bowtie2_index', 'GRCh38'))",

+            "", 

             sep="\n"))

 )

@@ -25,11 +25,15 @@ echo_out <- addMeta(

         date = Sys.Date(),

         example = paste(

             "## Get data from evaluting recipe",

-            "recipeLoad('echo_out', return = TRUE)",

+            "echo_out <- recipeLoad('echo_out')",

             "echo_out$input <- 'Hello World'",

             "echo_out$outfile <- 'echoHelloWorld'",

             "getData(echo_out, outdir = 'data/folder', notes = c('echo', 'hello', 'world'))",

+            "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('echo', 'hello'))",

+            "", 

             sep="\n"))

-

 )

@@ -38,12 +38,16 @@ ensembl_liftover <- addMeta(

         date = Sys.Date(),

         example = paste(

             "## Get data from evaluting recipe",

-            "recipeLoad('ensembl_liftover', return = TRUE)",

+            "ensembl_liftover <- recipeLoad('ensembl_liftover')",

             "ensembl_liftover$species <- 'human'",

             "ensembl_liftover$from <- 'GRCh37'",

             "ensembl_liftover$to <- 'GRCh38'",

             "getData(ensembl_liftover, outdir = 'data/folder', notes = c('grch37', 'grch38'))",

             "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('ensembl', 'GRCh37'))",

+            "", 

             "## Get data from Google bucket directly",

             "dataUpdate('data/folder', cloud=TRUE)",

             "dh <- dataSearch(c('ensembl', 'GRCh37'))", 

@@ -27,8 +27,13 @@ gcp_broad_gatk_hg19 <- addMeta(

         date = Sys.Date(),

         url = "https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg19/v0",

         example = paste(

-            "recipeLoad('gcp_broad_gatk_hg19', return = TRUE)",

+            "gcp_broad_gatk_hg19 <- recipeLoad('gcp_broad_gatk_hg19')",

             "gcp_broad_gatk_hg19$filename <- '1000G_omni2.5.b37.vcf.gz'",

             "getData(gcp_broad_gatk_hg19, outdir = 'data/folder', notes = c('gcp', 'broad', 'reference', 'hg19', 'v0', '1000G', 'omni2.5'))",

+            "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('gcp', 'broad', 'hg19'))",

+            "", 

             sep="\n"))

 )

@@ -26,8 +26,14 @@ gcp_broad_gatk_hg38 <- addMeta(

         date = Sys.Date(),

         url = "https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38/v0",

         example = paste(

-            "recipeLoad('gcp_broad_gatk_hg38', return = TRUE)",

+            "gcp_broad_gatk_hg38 <- recipeLoad('gcp_broad_gatk_hg38')",

             "gcp_broad_gatk_hg38$filename <- '1000G_omni2.5.hg38.vcf.gz'",

             "getData(gcp_broad_gatk_hg38, outdir = 'data/folder', notes = c('gcp', 'broad', 'reference', 'hg38', 'v0', '1000G', 'omni2.5')",

+            "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('gcp', 'broad', 'hg38'))",

+            "", 

+

             sep="\n"))

 )

@@ -27,9 +27,14 @@ gcp_gatk_mutect2_b37 <- addMeta(

         date = Sys.Date(),

         url = "https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-b37",

         example = paste(

-            "recipeLoad('gcp_gatk_mutect2_b37', return = TRUE)",

+            "gcp_gatk_mutect2_b37 <- recipeLoad('gcp_gatk_mutect2_b37')",

             "gcp_gatk_mutect2_b37$filename <- 'small_exac_common_3.vcf'",

             "gcp_gatk_mutect2_b37$idx <- 'idx'",

-            "getData(gcp_gatk_mutect2_b37, outdir = 'data/folder', notes = c('gcp', 'broad', 'mutect2', 'small_exac_common'))",

+            "getData(gcp_gatk_mutect2_b37, outdir = 'data/folder', notes = c('gcp', 'gatk', 'mutect2', 'b37', 'small_exac_common'))",

+            "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('gcp', 'gatk', 'b37'))",

+            "", 

             sep="\n"))

 )

@@ -26,9 +26,14 @@ gcp_gatk_mutect2_hg38 <- addMeta(

         date = Sys.Date(),

         url = "https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-hg38",

         example = paste(

-            "recipeLoad('gcp_gatk_mutect2_hg38', return = TRUE)",

+            "gcp_gatk_mutect2_hg38 <- recipeLoad('gcp_gatk_mutect2_hg38')",

             "gcp_gatk_mutect2_hg38$filename <- 'small_exac_common_3.hg38.vcf.gz'",

             "gcp_gatk_mutect2_hg38$idx <- 'tbi'",

-            "getData(gcp_gatk_mutect2_hg38, outdir = 'data/folder', notes = c('gcp', 'broad', 'mutect2', 'small_exac_common'))",

+            "getData(gcp_gatk_mutect2_hg38, outdir = 'data/folder', notes = c('gcp', 'gatk', 'mutect2', 'hg38', 'small_exac_common'))",

+            "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('gcp', 'gatk', 'hg38'))",

+            "", 

             sep="\n"))

 )

@@ -31,11 +31,15 @@ gencode_annotation <- addMeta(

         date = Sys.Date(),

         example = paste(

             "## Get data from evaluting recipe",

-            "recipeLoad('gencode_annotation', return = TRUE)",

+            "gencode_annotation <- recipeLoad('gencode_annotation')",

             "gencode_annotation$species <- 'human'",

             "gencode_annotation$version <- '42'",

             "getData(gencode_annotation, outdir = 'data/folder', notes = c('gencode', 'annotation', 'human', '42'))",

             "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('gencode', 'annotation', 'human', '42'))",

+            "", 

             "## Get data from Google bucket directly",

             "dataUpdate('data/folder', cloud=TRUE)",

             "dh <- dataSearch(c('gencode', 'annotation'))", 

@@ -17,9 +17,13 @@ gencode_genome_grch38 <- addMeta(

         date = Sys.Date(),

         example = paste(

             "Get data from evaluting recipe",

-            "recipeLoad('gencode_genome_grch38', return = TRUE)",

+            "gencode_genome_grch38 <- recipeLoad('gencode_genome_grch38')",

             "getData(gencode_genome_grch38, outdir = 'data/folder', notes = c('gencode', 'genome', 'grch38', 'release 42'))",

             "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('gencode', 'genome', 'grch38', '42'))",

+            "", 

             "## Get data from Google bucket directly",

             "dataUpdate('data/folder', cloud = TRUE)",

             "dh <- dataSearch(c('gencode', 'genome', 'grch38'))",

@@ -37,11 +37,15 @@ gencode_transcripts <- addMeta(

         date = Sys.Date(),

         example = paste(

             "## Get data from evaluating recipe",

-            "recipeLoad('gencode_transcripts', return = TRUE)",

+            "gencode_transcripts <- recipeLoad('gencode_transcripts')",

             "gencode_transcripts$species <- 'mouse'",

             "gencode_transcripts$version <- 'M31'",

             "getData(gencode_transcripts, outdir = 'data/folder', notes = c('gencode', 'transcripts', 'mouse', 'M31'))",

             "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('gencode', 'transcripts', 'mouse', 'M31'))",

+            "", 

             "## Get data from Google bucket directly",

             "dataUpdate('data/folder', cloud=TRUE)",

             "dh <- dataSearch(c('gencode', 'transcripts'))", 

@@ -25,8 +25,13 @@ hisat2_index <- addMeta(

         date = Sys.Date(),

         url = "http://daehwankimlab.github.io/hisat2/",

         example = paste(

-            "recipeLoad('hisat2_index.R', return = TRUE)",

+            "hisat2_index.R <- recipeLoad('hisat2_index.R')",

             "hisat2_index$genome <- 'GRCh38.primary_assembly.genome.fa'",

             "getData(hisat2_index, outdir = 'data/folder', notes = c('hisat2_index', 'GRCh38.primary_assembly'))",

+            "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('hisat2_index', 'GRCh38.primary_assembly'))",

+            "", 

             sep="\n"))

 )

@@ -66,10 +66,14 @@ reference_genome <- addMeta(

         date = Sys.Date(),

         example = paste(

             "## Get data from evaluating recipe",

-            "recipeLoad(reference_genome, return=TRUE)",

+            "reference_genome <- recipeLoad(reference_genome)",

             "reference_genome$fasta = 'http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.MT.fa.gz'",

             "getData(reference_genome, outdir = 'data/folder', notes = c('homo sapiens', 'grch38', 'ensembl'), conda = TRUE, docker = FALSE)",

             "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('homo sapiens', 'grch38', 'ensembl'))",

+            "", 

             "## Get data from Google bucket directly",

             "dataUpdate('data/folder', cloud=TRUE)",

             "dh <- dataSearch(c('homo sapiens', 'grch38', '1000 genomes'))", 

@@ -31,9 +31,14 @@ salmon_index <- addMeta(

         date = Sys.Date(),

         url = "https://salmon.readthedocs.io/en/latest/salmon.html",

         example = paste(

-            "recipeLoad('salmon_index.R', return = TRUE)",

+            "salmon_index <- recipeLoad('salmon_index.R')",

             "salmon_index$genome <- 'GRCh38.primary_assembly.genome.fa'",

             "salmon_index$transcript <- 'gencode.v42.transcripts.fa'",

             "getData(salmon_index, outdir = 'data/folder', notes = c('salmon_index', 'GRCh38.primary_assembly', 'gencode.v42'))",

+            "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('salmon_index', 'GRCh38.primary_assembly', 'gencode.v42'))",

+            "", 

             sep="\n"))

 )

@@ -28,9 +28,14 @@ ucsc_database <- addMeta(

         date = Sys.Date(),

         example = paste(

             "## Get data from evaluting recipe",

-            "recipeLoad('ucsc_database', return = TRUE)",

+            "ucsc_database <- recipeLoad('ucsc_database')",

             "ucsc_database$build <- 'hg38'",

             "ucsc_database$dbname <- 'refGene'",

             "getData(ucsc_database, outdir = 'data/folder', notes = c('ucsc', 'annotation', 'database', 'hg38', 'refGene'))",

+            "",

+            "## Get data from local catch",

+            "dataUpdate('data/folder')", 

+            "dataSearch(c('ucsc', 'annotation', 'database', 'hg38', 'refGene'))",

+            "", 

             sep="\n"))

 )