From 71d631c6c0904da57fb9b4036e41abaddbcb69c2 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <dominik.brilhaus@hhu.de>
Date: Mon, 21 Mar 2022 16:32:22 +0100
Subject: [PATCH] Update

---
 .gitattributes                 |  1 +
 README.md                      | 47 +++++++++++++++++-----------------
 workflows/.Rhistory            |  1 +
 workflows/06_plot_shinyApp.Rmd |  2 +-
 4 files changed, 27 insertions(+), 24 deletions(-)
 create mode 100644 workflows/.Rhistory

diff --git a/.gitattributes b/.gitattributes
index 2635f9c..60db50c 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1 +1,2 @@
 **/dataset/** filter=lfs diff=lfs merge=lfs -text
+/runs/run1/01_kallisto_index filter=lfs diff=lfs merge=lfs -text
diff --git a/README.md b/README.md
index 49cbdc8..eba9e1a 100644
--- a/README.md
+++ b/README.md
@@ -1,12 +1,14 @@
 # ARC mininmal Example RNASeq
 
-This is a minimal Example ARC packaging an mRNA-Seq dataset with metadata and computations. 
+This is a minimal Example ARC packaging an mRNA-Seq dataset with metadata and computations.
 
 ## Data origin
-- Partly published under: https://doi.org/10.1104/pp.15.01076
-- see [./isa.investigation.xlsx](./isa.investigation.xlsx) for details. 
+
+- Partly published under: <https://doi.org/10.1104/pp.15.01076>
+- see [./isa.investigation.xlsx](./isa.investigation.xlsx) for details.
 
 ## Additional payload
+
 > The following folders are not part of the ARC  
 > for details, see: [ARC specs:Additional paylod](https://github.com/nfdi4plants/ARC-specification/blob/main/ARC%20specification.md#additional-payload)
 
@@ -14,34 +16,33 @@ Directory | Purpose
 ---- | ----
 [_GEO_submission](./_GEO_submission) | Example metadata files as required for submission to GEO
 
-
 ## 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 
+- split GEO SWATE templates into four sheets
+  - 1SPL01_plants
+  - 2EXT01_RNA
+  - 3ASY01_RNASeq
+  - 4COM01_RNASeq
 
-1. Before addind the files to the ARC, track them via `git lfs`
-
-```
-git lfs track "*.fastq.gz"
-git lfs track "01_kallisto_index"
+### Adding large raw data via git lfs
 
-```
+1. Before addind the files to the ARC, track them via `git lfs`
 
-2. Move / add the large data files to the respective folders
+    ```bash
+    git lfs track "*.fastq.gz"
+    git lfs track "01_kallisto_index"    
+    ```
 
-3. Add them via `git add`
+1. Move / add the large data files to the respective folders
 
-```
-git add assays/Talinum_RNASeq_minimal/dataset/
-git add runs/run1/01_kallisto_index
+1. Add them via `git add`
 
-```
+    ```bash
+    git add assays/Talinum_RNASeq_minimal/dataset/
+    git add runs/run1/01_kallisto_index
+    
+    ```
 
-4. Commit
+1. Commit
diff --git a/workflows/.Rhistory b/workflows/.Rhistory
new file mode 100644
index 0000000..2682a56
--- /dev/null
+++ b/workflows/.Rhistory
@@ -0,0 +1 @@
+ARC_root="~/03_DataPLANT_gitlab/samplearc_rnaseq/"
diff --git a/workflows/06_plot_shinyApp.Rmd b/workflows/06_plot_shinyApp.Rmd
index d48a3b6..09b641d 100644
--- a/workflows/06_plot_shinyApp.Rmd
+++ b/workflows/06_plot_shinyApp.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(echo = TRUE)
 
 # Load data
 
-ARC_root="~/Hackathon_ARCexample_rnaseq/"
+ARC_root="~/03_DataPLANT_gitlab/samplearc_rnaseq/"
 load(file = paste0(ARC_root, 'runs/05_shinyPrep.RData'))
 
 ```
-- 
GitLab