rm upgrade README

README.md

@@ -38,4 +38,4 @@ assays/Talinum_RNASeq_minimal/isa.assay.xlsx | "RNA extraction" v. 1.1.6<br>"RNA
 
 Directory | Purpose
 ---- | ----
-[_GEO_submission](./_GEO_submission) | Example metadata files as required for submission to GEO
+[_GEO_submission](./_GEO_submission) | Example metadata files as required for submission to GEO
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README_arc_wip.md

-
-## Notes and ToDos
-
-### Experimental metadata in isa.assay.xlsx
-
-- split GEO SWATE templates into four sheets
-  - 1SPL01_plants
-  - 2EXT01_RNA
-  - 3ASY01_RNASeq
-  - 4COM01_RNASeq
-
-### Adding large raw data via git lfs
-
-1. Before adding the files to the ARC, track them via `git lfs`
-
-    ```bash
-    git lfs track "01_kallisto_index"    
-    ```
-
-1. Move / add the large data files to the respective folders
-
-1. Add them via `git add`
-
-    ```bash
-    git add runs/run1/01_kallisto_index    
-    ```
-
-1. Commit
-
-
-
-## Bumping to ARC v1.1 (23.03.2022)
-
-### by arcCommander / shell
-> 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
-
-arc assay register -s TalinumFacultativeCAM -a Talinum_RNASeq_minimal # re-register assay 
-arc update
-
-mv assays/Talinum_RNASeq_minimal/protocols/01_plant_material.md studies/TalinumFacultativeCAM/protocols # move plant growth from assay to study
-
-arc assay remove -s TalinumFacultativeCAM -a RNASeq_Kallisto_quant # add computational parts as assay 
-
-```
-
-
-### by hand
-- move plant growth sheet isa.assay to isa.study
-- remove computational RNASeq sheet from assays as it partly duplicates the (not yet CWLed) kallisto workflow
-
-### add placeholder sample descriptors
-
-```bash
-arc_root=$(pwd)
-cd studies/TalinumFacultativeCAM/resources/
-touch \
-DB_097 \
-DB_099 \
-DB_103 \
-DB_161 \
-DB_163 \
-DB_165
-cd $arc_root
-```
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