Commit 37ca0314 authored by Holger Brandl's avatar Holger Brandl

adjusted to use new .logs directory

parent 129c852e
......@@ -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
mkdir $newVersion
cd $newVersion
git clone git-srv1:/local/git/bioinformatics .
git checkout ${newVersion}
## prevent from writing
chmod -R -w ../$newVersion
......@@ -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>")
......@@ -31,7 +31,7 @@ if($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)
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