added start tests

dge_workflow/star_align.kts

@@ -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 &
+""")

dge_workflow/testdata/featcounts_deseq/test_star.sh

+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"
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