renamed DGE_HOME to NGS_TOOLS

dge_workflow/README.md

-# RNA-Seq DGE Workflow
-
-git checkout-index -a -f --prefix=/destination/path/
-
-## How to use install it?
-
-export the directory from git into your project
-git archive --format=tar --remote=git-srv1:/local/git/bioinformatics master dge_workflow/ | tar -xf -
-
-http://stackoverflow.com/questions/160608/do-a-git-export-like-svn-export
-
-or
-
-do a sparse checkout (not recommenced without solid understandng how git works)
-http://stackoverflow.com/questions/600079/is-there-any-way-to-clone-a-git-repositorys-sub-directory-only
-
-cd /somewhere
-git init
-git remote add origin git-srv1:/local/git/bioinformatics
-git config core.sparsecheckout true
-echo "dge_workflow/" >> .git/info/sparse-checkout
-git pull origin master
-
-## How to use it?
-
-1) Copy dge_master_template.sh into and rename into something meaningful (e.g. dge_mouse_helin.sh)
-2) Adjust DGE_HOME in master script
-3) Run on madmax
-4) Adjust reports if necessary
-
-
-## How to backport changes into it?
-
-Clone it, change it, push and commit it.

dge_workflow/RnaSeq_Howto.md

+# RNA-Seq DGE Workflow
+
+## todo write this!!
\ No newline at end of file

dge_workflow/dge_master_template.sh

@@ -7,7 +7,7 @@ export project=<<PROJECTNAME>>
 if [ -n "$LSF_SERVERDIR" ]; then
     export baseDir="/projects/bioinfo/holger/projects/${project}"
     export PROJECT_SCRIPTS="/projects/bioinfo/holger/scripts/${project}"
-    export DGE_HOME="/projects/bioinfo/scripts/ngs_tools/v1.0/"
+    export NGS_TOOLS="/projects/bioinfo/scripts/ngs_tools/v1.1"
 fi
 
 ## bioinfo
@@ -15,12 +15,12 @@ if [ $(hostname) == "bioinformatics-srv1" ]; then
     #<<<todo define paths on bioinfo>>>
     #export baseDir=/home/brandl/mnt/chip-seq_study/ChIPSeq_March_2015/data
     #export PROJECT_SCRIPTS=/home/brandl/mnt/chip-seq_study/ChIPSeq_March_2015/scripts
-    export DGE_HOME="/home/brandl/mnt/mack/bioinfo/scripts/ngs_tools/v1.0"
+    export NGS_TOOLS="/home/brandl/mnt/mack/bioinfo/scripts/ngs_tools/v1.1"
 fi
 
 
-source $DGE_HOME/dge_workflow/dge_utils.sh
-export PATH=$DGE_HOME/dge_workflow:$PATH
+source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
+export PATH=${NGS_TOOLS}/dge_workflow:$PATH
 
 
 ## todo define igenome to be used
@@ -40,12 +40,12 @@ mailme "$project: fastq download done"
 ## todo make sure to also copy the sample sheet in here
 
 ########################################################################################################################
-### QC
+### Basic QC
 
 dge_fastqc $(ls *fastq.gz) &
 
 ########################################################################################################################
-### Apply renaming and merge lane replicates (but keep technical ones)vvv
+### Apply renaming and merge lane replicates (but keep technical ones)
 
 ## todo adjust renaming scheme to project specifics
 
@@ -136,7 +136,7 @@ mailme "$project: mapping done"
 ### bio_reps="ctrl,isnm1"
 #
 #dge_merge_treps $baseDir/mapped/ $bio_reps
-#
+
 
 ########################################################################################################################
 ### Do the differential expression analysis
@@ -157,12 +157,12 @@ mailme "$project: cuffdiff done"
 
 mcdir $baseDir/cuffdiff/dge_report
 
-spin.R $DGE_HOME/cuffdiff_report.R ..
+spin.R ${NGS_TOOLS}/dge_workflow/cuffdiff_report.R ..
 
 ## or when using specfic contrasts
 #echo "Ctrl_12h,X11B_12h
 #Ctrl_36h,X11B_36h" > contrasts.txt
-#spin.R $DGE_HOME/cuffdiff_report.R  \""--constrasts contrasts.txt --pcutoff 0.01 $baseDir/cuffdiff"\"
+#spin.R $NGS_TOOLS/dge_workflow/cuffdiff_report.R  \""--constrasts contrasts.txt --pcutoff 0.01 $baseDir/cuffdiff"\"
 
 
 

dge_workflow/dge_utils.sh

@@ -67,9 +67,8 @@ done
 
 wait4jobs .fastqc_jobs
 
-ziprm fastqc_logs fastqc__*.log
 
-spin.R $DGE_HOME/fastqc_summary.R $outputDir
+spin.R ${NGS_TOOLS}/dge_workflow/fastqc_summary.R $outputDir
 
 mailme "$project: fastqc done in $(pwd)"
 
@@ -92,9 +91,8 @@ done
 
 wait4jobs .cajobs
 
-spin.R $DGE_HOME/cutadapt_summary.R .
+spin.R ${NGS_TOOLS}/dge_workflow/cutadapt_summary.R .
 
-ziprm cutadapt_logs ${project}__ca__*.log
 
 
 ## todo do a small report here about what has been trimmed away and why
@@ -164,13 +162,12 @@ done
 
 wait4jobs .tophatjobs
 
-ziprm tophat_logs ${project}__tophat__*.log
 
 
 dge_bam_correlate .
 
 ## create tophat mapping report
-spin.R $DGE_HOME/tophat_qc.R .
+spin.R ${NGS_TOOLS}/dge_workflow/tophat_qc.R .
 
 mailme "$project: tophat done in $(pwd)"
 
@@ -275,7 +272,7 @@ local bamDir=$2
 local labels=$3
 
 if [ $# -ne 3 ]; then
-    echo "Usage: dge_fastqc <gtf_file>  <bam_directory> <labels>" >&2 ; return;
+    echo "Usage: dge_cuffdiff <gtf_file>  <bam_directory> <labels>" >&2 ; return;
 fi
 
 if [ -z "$(which cuffdiff)" ]; then