migrated bc wrapper to jl

dge_workflow/dge_utils.sh

@@ -195,22 +195,23 @@ if [ $# -eq 0 ]; then
     return;
 fi
 
-local bamDir=$1
 
-if [ $# -e 1 ]; then
-    bamFiles=$(find $bamDir | grep ".bam$" | grep -v "unmapped" | sort)
+if [ $# -eq 1 ]; then
+    bamFiles=$(find $1 | grep ".bam$" | grep -v "unmapped" | sort)
 else
     bamFiles=$*
 fi
 
-bamLabels=$(echo "$bamFiles" | xargs -n1 basename | sed 's!.*/!!' | sed 's/_mmf.bam//g' |  sed 's/_ca.bam//g' | sed 's/.bam//g' | xargs echo); echo $bamLabels
+local bamLabels=$(echo "$bamFiles" | xargs -n1 basename | sed 's!.*/!!' | sed 's/_mmf.bam//g' |  sed 's/_ca.bam//g' | sed 's/.bam//g' | xargs echo);
+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=6 --corMethod spearman --zMin 0.5 --zMax 1"
-echo $bcCmd
+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"
+#echo "cmd is $bcCmd"
 #mysub "${project}__bamcorrelate" "$bcCmd"  -q long -n 4 -R span[hosts=1] | blockScript .bamcorrelate
-#mailme "$project: bamcorrelate done in $(pwd)"
+
+jl submit --wait --jl .bamcorrelate -q long -t 4 -n "${project}__bamcorrelate" "$bcCmd"
 
 }
 export -f dge_bam_correlate

dge_workflow/star_qc.R

@@ -120,7 +120,7 @@ algnSummaryLong %>% filter(str_detect(variable, "Uniquely_mapped_reads_Perc|Perc
 #' ## Alignment Correlation
 
 #' Without using any transcriptome as reference, the genome can be binned and alignment counts per bin can be used to perform a correlation analysis.
-#' Used tool [deepTools](https://github.com/fidelram/deepTools)
+#' Created using [deepTools](https://github.com/fidelram/deepTools)
 
 ## http://stackoverflow.com/questions/291813/recommended-way-to-embed-pdf-in-html
 #+ results="asis"

dge_workflow/tophat_qc.R

@@ -79,7 +79,7 @@ ggplot(algnSummary, aes(condition, mapped_reads)) +
 #' ## Alignment Correlation
 
 #' Without using any transcriptome as reference, the genome can be binned and alignment counts per bin can be used to perform a correlation analysis.
-#' Used tool [deepTools](https://github.com/fidelram/deepTools)
+#' Created using [deepTools](https://github.com/fidelram/deepTools)
 
 ## http://stackoverflow.com/questions/291813/recommended-way-to-embed-pdf-in-html
 #+ results="asis"