improved dge template

dge_workflow/dge_master_template.sh

@@ -147,11 +147,12 @@ dge_merge_treps $baseDir/mapped/ $bio_reps
 mcdir $baseDir/cuffdiff
 
 gtfFile=$igenome/Annotation/Genes/genes.gtf
+head $gtfFile
 
 ## define labels to split bam files into replicate groups
-#labels=$(csvcut -t -c1 $baseDir/lanereps_pooled/sample2replicates.txt | tail -n+2 | uniq | xargs echo | sed 's/ /,/g')
-## better externalize them
-labels=<<<<TBD>>>>
+labels=$(csvcut -t -c1 $baseDir/lanereps_pooled/sample2replicates.txt | tail -n+2 | uniq | xargs echo | sed 's/ /,/g')
+## todo better externalize them
+#labels=<<<<TBD>>>>
 
 dge_cuffdiff $gtfFile $baseDir/mapped $labels
 
@@ -171,15 +172,10 @@ spin.R $DGE_HOME/cuffdiff_report.R ..
 ########################################################################################################################
 ### Sync back to project space
 
-# uni
-screen -R rsync_$project
-
-## main sync
+## bidirectional sync with project space
 ## todo define mount path on bioinfo for bidirectional synching
 ~/bin/unison $baseDir ssh://bioinfo///home/brandl/mnt/<<MOUNT_PATH>> -fastcheck true -times -perms 0
 
-
-rsync -avsn --delete  $baseDir brandl@fileserver:/projects//file/server/path
-
-mailme "$project: rsync done"
+# uni-directional sync
+#rsync -avsn --delete  $baseDir brandl@fileserver:/projects//file/server/path
+mailme "$project: sync done"
\ No newline at end of file
-

dge_workflow/dge_utils.sh

@@ -2,12 +2,14 @@
 ## http://blog.joncairns.com/2013/08/what-you-need-to-know-about-bash-functions/
 
 ## load lsf helpers
-source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/bash/lsf_utils.sh 2>&1 2>/dev/null)
+source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.10/bash/lsf_utils.sh 2>&1 2>/dev/null)
 
 ## enable snippet spinning
-source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/master/R/spinr/spin_utils.sh 2>&1 2>/dev/null)
+source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.10/R/spinr/spin_utils.sh 2>&1 2>/dev/null)
+
 
 ## define common binaries
+## todo tweak this to work on bioinfo as well
 export PATH=/projects/bioinfo/holger/bin/bowtie2-2.2.2:$PATH
 export PATH=/projects/bioinfo/holger/bin/tophat-2.0.13.Linux_x86_64:$PATH
 export PATH=/home/brandl/bin/cufflinks-2.2.1.Linux_x86_64:$PATH