Commit dc74d040 authored by Holger Brandl's avatar Holger Brandl

added start tests

parent 6b5fcd52
......@@ -42,12 +42,19 @@ 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")
println("validating inputs...")
println("validating system requirements...")
// make sure that STAR is in the PATH
if (evalBash("which STAR").exitCode != 0) throw IllegalArgumentException("STAR aligner is not in PATH")
System.getenv("NGS_TOOLS").let {
require(it.isNotBlank() && File(it).isDirectory) { "NGS_TOOLS is not defined but needed to locate star_qc.R" }
}
require(evalBash("type dge_star_counts2matrix").exitCode==0) {"dge_star_counts2matrix is missing"}
require(evalBash("type dge_bam_correlate").exitCode==0){"dge_bam_correlate is missing"}
println("validating inputs...")
// check if gtf file exists
if (!gtfFile.isFile()) throw IllegalArgumentException("gtf '${gtfFile}' does not exist")
......@@ -112,11 +119,14 @@ joblist.`package$`.`MODULE$`.ImplJobListUtils(jl).createHtmlReport()
// cleanup
evalBash("""rm - rf * STARgenome * .Log.progress.out _STARtmp * .SJ.out.tab *Log.out""")
// Test for bam correlation (but don't wait for the results)
// Do reporting and perform bam correlation (but don't wait for the results)
evalBash("""
rend.R - e ${ System.getenv("NGS_TOOLS") } / dge_workflow / star_qc.R.
dge_bam_correlate &
""")
rend.R - e ${'$'}NGS_TOOLS / dge_workflow / star_qc.R.
// Condense counts into matrix
evalBash("""dge_star_countas2matrix""")
# Condense counts into matrix
dge_star_counts2matrix
# http://superuser.com/questions/178587/how-do-i-detach-a-process-from-terminal-entirely
nohup dge_bam_correlate &
#dge_bam_correlate &
""")
screen -R star_test
cd /home/brandl/test_star_kot
export NGS_TOOLS="/home/brandl/mnt/mack/bioinfo/scripts/ngs_tools/dev"
export PATH=/home/brandl/bin/STAR-2.5.1b/source:$PATH
export PATH=${NGS_TOOLS}/dge_workflow:$PATH
source $NGS_TOOLS/dge_workflow/dge_utils.sh
#git clone https://github.com/holgerbrandl/kutils && cd kutils && gradle install && cd .. && rm -rf kutils
star_align.kts /local2/igenomes/Mus_Musculus/Ensembl/GRCm38 test.fastq
mailme "test"
\ No newline at end of file
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