Add download instruction

README.md

@@ -74,9 +74,32 @@ This project uses Python 3 and PyYAML. These may be installed with [`conda`](htt
 
 ## User manual
 
-### 1. Preparing data
+### 1. Download the pipeline
 
-#### Importing from Jovian
+To download the pipeline from this page, use git clone:
+
+```bash
+git clone git@git.lumc.nl:snooij/jovian-screener.git
+```
+
+(Also see the 'Clone' button at the top of this page for the SSH and HTTPS links.)  
+Then, optionally change the name of the newly downloaded directory:
+
+```bash
+mv jovian-screener My_new_project
+```
+
+And change directory into this new project to get started:
+
+```bash
+cd My_new_project
+```
+
+_(N.B. Change 'My_new_project' to whatever name you like for your directory!)_
+
+### 2. Prepare data
+
+#### Import from Jovian
 
 This project includes a Python script that can import all required output files from Jovian into the desired new project directory. 
 _This is the recommended way of importing data._
@@ -85,22 +108,28 @@ To use it, one needs to have run Jovian and preferably have created a new direct
 Also, the script requires PyYAML to be installed. 
 If you did this with conda, activate the corresponding conda environment before running the next commands, e.g.:
 
-`conda activate pyyaml`
+```bash
+conda activate pyyaml
+```
 
 If you are currently in this new directory, which sits next to the Jovian directory, called `Jovian`, the importer script can be used as follows:
 
-`bin/import_jovian_output.py -i ../Jovian/ -o ./`
+```bash
+bin/import_jovian_output.py -i ../Jovian/ -o ./
+```
 
 (Where `-i` stands for input, `../Jovian/` points to Jovian's main directory or folder,
 `-o` stands for output, and `./` is the current working directory.)
 
 By default, the script will move the files from Jovian's directory. If you want to make a new copy, instead use:
 
-`bin/import_jovian_output.py -i ../Jovian/ -o ./ -m copy`
+```bash
+bin/import_jovian_output.py -i ../Jovian/ -o ./ -m copy
+```
 
 (Where `-m` can be used to select the mode: copy, move or link.)
 
-#### Choosing a reference
+#### Choose a reference
 
 The data to be screened is now ready. Next up is the sequence and/or species to be screened for.
 This sequence should be saved (in fasta format) and the file path should be added to the configuration file `config/config.yaml` in the line that starts with `reference: `.