From 3545e72471780d20ec20b40d3783a1aca2172b8a Mon Sep 17 00:00:00 2001 From: Dominik <dominik.brilhaus@hhu.de> Date: Wed, 23 Mar 2022 21:20:23 +0100 Subject: [PATCH] set structure, reshuffle, remove deprecated --- README.md | 26 ++++++++++++++---- inv.json | 1 - isa.investigation.xlsx | Bin 14525 -> 4828 bytes studies/TalinumFacultativeCAM/README.md | 0 studies/TalinumFacultativeCAM/isa.study.xlsx | Bin 0 -> 3150 bytes .../TalinumFacultativeCAM/old.study.xlsx | Bin .../TalinumFacultativeCAM/protocols/.gitkeep | 0 .../TalinumFacultativeCAM/resources/.gitkeep | 0 .../TalinumGenomeDraft}/README.md | 0 studies/TalinumGenomeDraft/isa.study.xlsx | Bin 0 -> 3143 bytes studies/TalinumGenomeDraft/protocols/.gitkeep | 0 studies/TalinumGenomeDraft/resources/.gitkeep | 0 12 files changed, 21 insertions(+), 6 deletions(-) delete mode 100644 inv.json create mode 100644 studies/TalinumFacultativeCAM/README.md create mode 100644 studies/TalinumFacultativeCAM/isa.study.xlsx rename TalinumFacultativeCAM.study.xlsx => studies/TalinumFacultativeCAM/old.study.xlsx (100%) create mode 100644 studies/TalinumFacultativeCAM/protocols/.gitkeep create mode 100644 studies/TalinumFacultativeCAM/resources/.gitkeep rename {externals => studies/TalinumGenomeDraft}/README.md (100%) create mode 100644 studies/TalinumGenomeDraft/isa.study.xlsx create mode 100644 studies/TalinumGenomeDraft/protocols/.gitkeep create mode 100644 studies/TalinumGenomeDraft/resources/.gitkeep diff --git a/README.md b/README.md index eba9e1a..878fe5f 100644 --- a/README.md +++ b/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 +``` \ No newline at end of file diff --git a/inv.json b/inv.json deleted file mode 100644 index 345003d..0000000 --- a/inv.json +++ /dev/null @@ -1 +0,0 @@ -{"identifier":"Hackathon_ARCexample_rnaseq","title":"Facultative CAM in Talinum triangulare","submissionDate":"July 07, 2015","publicReleaseDate":"Nov 05, 2015","publications":[{"pubMedID":"26530316","doi":"10.1104/pp.15.01076","authorList":"Brilhaus, Dominik; Bräutigam, Andrea; 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