From d98548bce6a6886a785e2a0cdac74265216eb626 Mon Sep 17 00:00:00 2001
From: Dominik <dominik.brilhaus@hhu.de>
Date: Wed, 24 Aug 2022 15:32:47 +0200
Subject: [PATCH] update readme

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 # CEPLAS RNASeq Workshop 2022
 
-This ARC provides the all course material required for the CEPLAS RNASeq Workshop 2022. Please explore the [Reader](_reader/RNAseqWorkshop.pdf) for details. 
+This ARC provides all course material required for the CEPLAS RNASeq Workshop (August 22 - 24, 2022).
+Please explore the [Reader](_reader/RNAseqWorkshop.pdf) for details.
 
+## More information about ARCs in general
 
-- Docker images at sciebo
-  - https://uni-duesseldorf.sciebo.de/s/53pA9W9TbOKTgGQ
-  - See reader section 4.3 for details
-  - Password provided via email or during class.  
-  
-- Notes collected during the workshop: https://pad.hhu.de/Qlsi4q9fQ9-YPmzv6Ryeog
+Please visit the [DataPLANT website](https://nfdi4plants.org).
+
+## The basic ARC structure summarized
+
+directory | content
+------- | -------
+[studies](studies) | external data and sample metadata
+[assays](assays) | measurement data (i.e. "raw" sequence data) and metadata
+[workflows](workflows) | computational analyses (i.e. "scripts")
+[runs](runs) | outputs of workflow | (i.e. "results")
+
+## Material added to the ARC for this course
+
+directory | content
+------- | -------
+[_reader](_reader/) | The basis to this reader (written in LaTeX)
+[_slides](_slides/) | Slides presented during the workshop
+[_handouts](_handouts/) | Cheat sheets and additional materials
+[runs/_backups](runs/_backup/) |  Backups for runs, in case a workflow unexpectedly did not work or takes too long
+
+## Docker
+
+In order to use the tools and run all scripts mentioned in the reader, you need to install some dependencies on your machine.
+This is done using the docker images available at sciebo or built from scratch.
+
+### Ready to use docker images
+
+...can be downloaded from sciebo
+
+- https://uni-duesseldorf.sciebo.de/s/53pA9W9TbOKTgGQ
+- See reader section 4.3 for details
+- Password provided via email or during class
+
+### Build docker image
+
+If you want to build the docker images from scratch (rather than downloading from sciebo), follow the respective instructions in
+ 
+ - [workflows/maindocker](workflows/maindocker)
+ - [workflows/rstudiodocker](workflows/rstudiodocker)
+ - [workflows/userdocker](workflows/userdocker)
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-- 
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