adjusted to use new .logs directory

README.md

@@ -46,15 +46,23 @@ How to create a new version tag
 1.  Create branch:
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+cd /Volumes/projects/bioinfo/scripts/ngs_tools/dev
 git checkout -b v3.23
+git push
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-1.  Checkout branch into ngs\_tools
+1.  Checkout new branch into ngs\_tools as stable version
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 cd /Volumes/projects/bioinfo/scripts/ngs_tools/
-mkdir v3.23
-git clone  —> git checkout v3.23
+newVersion=v1.1
+mkdir $newVersion
+cd $newVersion
+git clone git-srv1:/local/git/bioinformatics .
+git checkout ${newVersion}
+
+## prevent from writing 
+chmod -R -w ../$newVersion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
  

dge_workflow/cutadapt_summary.R

@@ -17,7 +17,7 @@ argv = commandArgs(TRUE)
 #if(str_detect(argv[1], "fastqc_summary")) argv <- argv[-1]
 
 if(length(argv) != 1){
-  stop("Usage: First_try.R <directory with cutadapt log files>")
+  stop("Usage: cutadapt_summary.R <directory with cutadapt log files>")
 }
 
 baseDir=argv[1]
@@ -31,7 +31,7 @@ if(is.na(file.info(baseDir)$isdir)){
 # baseDir="/home/mel/MPI-Bioinf/Project1_reads/141126_cutadapt_logs"
 
 
-logDataFiles <- list.files(path=baseDir, pattern="__ca__.*.out.log", full.names=TRUE, recursive=T)
+logDataFiles <- list.files(path=file.path(baseDir, ".logs"), pattern="__ca__.*.out.log", full.names=TRUE, recursive=T)
 
 #echo("files are", logDataFiles)