## gencode_transcripts
script <- "
species=$1
version=$2
if [ $species == 'human' ] && [ $version -gt 22 ]
then
trans='transcripts'
else
trans='pc_transcripts'
fi
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_$species/release_$version/gencode.v$version.$trans.fa.gz
gzip -d gencode.v$version.$trans.fa.gz
samtools faidx gencode.v$version.$trans.fa
"
gencode_transcripts <- recipeMake(script,
paramID = c("species", "version"),
paramType = c("string", "string"),
outputID = "transcripts",
outputGlob = "*transcripts.fa*")
gencode_transcripts <- addMeta(
cwl = gencode_transcripts,
label = "gencode_transcripts",
doc = "Download, unzip, and index transcripts files from gencode",
inputLabels = c("species", "version"),
inputDocs = c("'human' or 'mouse'",
paste0("Character string. Case sensitive. ",
"must match available versions for each species under source URL link. ",
"e.g., 'M31' (species='mouse'), '42' (species='human') ")),
outputLabels = c("transcripts"),
outputDocs = c("the samtool indexed annotation files: `*transcripts.fa`, `*transcripts.fa.fai`"),
extensions = list(
author = "rworkflow team",
url = "http://ftp.ebi.ac.uk/pub/databases/gencode/",
date = Sys.Date(),
example = paste(
"## Get data from evaluating recipe",
"gencode_transcripts <- recipeLoad('gencode_transcripts')",
"gencode_transcripts$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'))",
"getCloudData(dh[1], outdir = 'data/folder')",
sep="\n"))
)
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