updated bam correlation to work with latest deeptools. @lakshman v2.2.2 of...

updated bam correlation to work with latest deeptools. @lakshman v2.2.2 of deeptools is required now to run the star-workflow

dge_workflow/dge_utils.sh

@@ -242,7 +242,12 @@ echo "Used bam labels are: $bamLabels"
 
 
 ## see how well bam files correlate using untrimmed data
-bcCmd="bamCorrelate bins --bamfiles $(echo $bamFiles | xargs echo) --labels $bamLabels --plotFile=bc.pdf --outFileCorMatrix=bc.txt --numberOfProcessors=4 --corMethod spearman --zMin 0.5 --zMax 1"
+# http://deeptools.readthedocs.org/en/latest/content/tools/multiBamSummary.html
+# http://deeptools.readthedocs.org/en/latest/content/tools/plotCorrelation.html?highlight=plotfile
+bcCmd="
+multiBamSummary bins --bamfiles $(echo $bamFiles | xargs echo) --labels $bamLabels -out bam_cor_matrix.txt --numberOfProcessors 4
+plotCorrelation --corData bam_cor_matrix.txt --plotFile bc.pdf --corMethod spearman --zMin 0.5 --zMax 1 -p heatmap
+"
 #echo "cmd is $bcCmd"
 #mysub "${project}__bamcorrelate" "$bcCmd"  -q long -n 4 -R span[hosts=1] | blockScript .bamcorrelate
 

dge_workflow/star_align.kts

@@ -72,7 +72,7 @@ fastqFiles.filter { !it.isFile }.let {
     require(it.isEmpty()) { "Some fastq files do not exist  ${it.map { it.absoluteFile }.joinToString(", ")}" }
 }
 
-println("running STAR using igenome '${igenome}' for the following files")
+println("Running STAR using igenome '${igenome}' for the following files:\n ${fastqFiles.joinToString("\n")}")
 
 val jl = JobList(".starjobs")
 

tool_setup.sh

+cd ~/bin
+wget -O deepTools-2.2.2.tar.gz  https://github.com/fidelram/deepTools/archive/2.2.2.tar.gz
+tar xvf deepTools-2.2.2.tar.gz
+cd deepTools-2.2.2
+
+python setup.py install --user
\ No newline at end of file