adopted fc dba analysis for new data.

chipseq_workflow/chipseq_utils.sh

@@ -110,10 +110,10 @@ done
 wait
 
 echo '
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/core_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/ggplot_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/ggplot_commons.R")
 
-libSizes <- read.delim("algn_counts.txt", header=F) %>% set_names(c("library_size", "sample"))
+libSizes <- read_tsv("algn_counts.txt", col_names=F) %>% set_names(c("library_size", "sample"))
 libSizes %>% ggplot(aes(sample, library_size)) +
     geom_bar(stat="identity") +
     ggtitle("algn_counts") +

dge_workflow/dge_utils.sh

@@ -61,6 +61,15 @@ mailme(){
 }
 export -f mailme
 
+ziprm(){
+    if [ $# -lt 2 ]; then echo "Usage: ziprm <tarbasename> [<file>]+"; return; fi
+
+    tarName=$(date +'%y%m%d')_"$1".tar.gz; shift
+    tar czf $tarName $@; rm $@;
+}
+export -f ziprm
+
+
 
 ## no longer needed because packages are no kept in home
 #export R_LIBS=/tmp/r_index ## export to make sure that packages are load from local repository, otherwise sqlite won't work