Commit 740c4ae0 authored by Holger Brandl's avatar Holger Brandl

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
parent 44ecad36
......@@ -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
......
......@@ -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")
......
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
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