set structure, reshuffle, remove deprecated

README.md

@@ -28,10 +28,9 @@ Directory | Purpose
 
 ### Adding large raw data via git lfs
 
-1. Before addind the files to the ARC, track them via `git lfs`
+1. Before adding the files to the ARC, track them via `git lfs`
 
     ```bash
-    git lfs track "*.fastq.gz"
     git lfs track "01_kallisto_index"    
     ```
 
@@ -40,9 +39,26 @@ Directory | Purpose
 1. Add them via `git add`
 
     ```bash
-    git add assays/Talinum_RNASeq_minimal/dataset/
-    git add runs/run1/01_kallisto_index
-    
+    git add runs/run1/01_kallisto_index    
     ```
 
 1. Commit
+
+
+
+## Bumping to ARC v1.1 (23.03.2022)
+
+> depends on arcCommander v3 or higher
+
+```bash
+arc a list
+
+arc study unregister -s TalinumFacultativeCAM # unregister old study version
+arc study add -s TalinumFacultativeCAM # add fresh
+mv TalinumFacultativeCAM.study.xlsx studies/TalinumFacultativeCAM/old.study.xlsx # move old study metadata to new study
+
+arc study add -s TalinumGenomeDraft # add draft genome as study
+mv externals/Talinum.gm.CDS.nt.fa studies/TalinumGenomeDraft/resources # mv genome to resources
+rm -r externals
+rm inv.json
+```
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