Commit 342c00c5 authored by Holger Brandl's avatar Holger Brandl

fixed incorrect wall time

parent 944e014f
......@@ -49,9 +49,9 @@ dge_fastqc $(ls *fastq.gz) &
mcdir $baseDir/lanereps_pooled
echo '
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.10/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/core_commons.R")
options(java.parameters = "-Xmx4g" ); library(xlsx)
options(java.parameters = "-Xmx4g" ); require_auto(xlsx)
sheetFile <- "../originals/natalied-FC_SN678_338-2015-5-12.xls"
......
......@@ -37,7 +37,7 @@ val doArgs = Docopt(usage).parse(args.toList()).map {
//doArgs["fastq_files"]
// extract all configuration parameters
val fastqFiles = (doArgs["fastq_files"] as String).substring(1).substringBefore("]").split(" ").map { File(it) }
val fastqFiles = (doArgs["fastq_files"] as String).substring(1).substringBefore("]").split(", ").map { File(it) }
val igenome = File(doArgs["igenome"])
val star_index = File(igenome, "Sequence/StarIndex")
val gtfFile = if (doArgs["gtfFile"] != null) File(doArgs["gtfFile"]) else File(igenome, "Annotation/Genes/genes.gtf")
......@@ -65,7 +65,9 @@ if (!File("${star_index}/SA").isFile())
// dge_create_star_index ${igenome}'
// make sure all fastq files do exist
//println("files are ${fastqFiles.joinToString(", ")}")
// make sure all fastq files do exist (for symlinks see http://www.java2s.com/Code/Java/JDK-7/Isfileasymboliclink.htm
//fastqFiles.filter { !(it.exists() || Files.isSymbolicLink(it.toPath())) }.let {
fastqFiles.filter { !it.isFile }.let {
require(it.isEmpty()) { "Some fastq files do not exist ${it.map { it.absoluteFile }.joinToString(", ")}" }
}
......@@ -95,7 +97,7 @@ for (fastqFile in fastqFiles) {
samtools index ${fastqBaseName}.bam
""".trimIndent()
jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", null, "medium", 5, "", better.files.File(File(".").toPath())))
jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", "", "medium", 5, "", better.files.File(File(".").toPath())))
}
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment