Big update : Add Rpackage, Add peak max coverage, Add mean coverage calc, Add...

Big update : Add Rpackage, Add peak max coverage, Add mean coverage calc, Add Tars scripts, Optimize whole workflow

INSTALL.txt

@@ -69,6 +69,15 @@ conda config --add channels conda-forge
 conda config --add channels bioconda
 conda create --name rscript python
 source activate rscript
+
+conda install bioconductor-genomicranges
+conda install bioconductor-rtracklayer
+conda install bioconductor-biomart
+conda install bioconductor-edger
+conda install bioconductor-genomicfeatures
+
+
+
 conda install r-sartools
 conda install bioconductor-sva
 # in R

src/bash/peak_detection.sh

@@ -36,7 +36,7 @@ WINDOW_CUTOFF=10  # 10 reads minimum in windows
 
 if $MACS2_STEP; then
 	if [[ " $peak_technique " == *" MACS2 "* ]]; then
-		outfolder=$folder/PeakDetection/MACS2/
+		outfolder=$folder/PeakDetection/temp/
 		module add macs/2.1.0
 		echo "Run MACS2 peak detection for" $biocond
 		macs2 callpeak -t $folder/Mapping/${ip_data}.bam -c $folder/Mapping/${input_data}.bam -n $biocond -f 'BAM' -g 282000000 --nomodel --outdir $outfolder

src/bash/setup.sh

@@ -92,6 +92,11 @@ if [ ! -d $temp_folder ]; then
 	mkdir $temp_folder
 fi
 
+temp_folder=$folder'/PeakDetection/temp/'
+if [ ! -d $temp_folder ]; then
+	mkdir $temp_folder
+fi
+
 temp_folder=$folder'/PeakDetection/Peaks/'
 if [ ! -d $temp_folder ]; then
 	mkdir $temp_folder