Improve README

README.md

@@ -22,30 +22,26 @@ Windows users can use the Windows Subsystem for Linux (WSL) to install AUGUSTUS
 
 ## Ubuntu 18.04 or later
 This currently installs only a single-genome version without comparative gene prediction capability:
-```
-sudo apt install augustus augustus-data augustus-doc
-```
+
+    sudo apt install augustus augustus-data augustus-doc
+
 
 ## Clone from GitHUB
 
 To obtain the most recent complete version, first, clone the repository
 
-```
-git clone https://github.com/Gaius-Augustus/Augustus.git
-```
+    git clone https://github.com/Gaius-Augustus/Augustus.git
+
 or, alternatively, [download](http://bioinf.uni-greifswald.de/augustus/binaries/augustus.current.tar.gz) and unpack the AUGUSTUS source package with
-```
-tar -xzf augustus.current.tar.gz
-```
+
+    tar -xzf augustus.current.tar.gz
 
 ## Docker
 
 After retrieving Augustus change into the main directory containing the 
 [Dockerfile](Dockerfile) and issue
 
-```
-docker build -t augustus .
-```
+    docker build -t augustus .
 
 ## Install dependencies
 
@@ -76,37 +72,33 @@ The following dependencies are required for AUGUSTUS:
 
 Once all dependencies are available, you can compile AUGUSTUS using make.
 
-```
-make
-```
+    make
 
 After compilation has finished, the command bin/augustus should be executable and print a usage message.
 
+If you have built the Boost libraries yourself, specify the search path for the linker in `LDFLAGS`.
+
+    make LDFLAGS="-L/your/boost_1_75_0/stage/lib"
+
 ## Install locally
 
 As a normal user, add the directory of the executables to the PATH environment variable, for example:
 
-```
-export PATH=$PATH:~/augustus/bin:~/augustus/scripts
-```
+    export PATH=~/augustus/bin:~/augustus/scripts:$PATH
 
 ## Install globally
 
 You can install AUGUSTUS globally, if you have root privileges, for example: 
 
-```
-sudo make install
-```
+    sudo make install
 
 Alternatively, you can exectue similar commands to those in the "install" section of the top-level Makefile to customize the global installation. 
 
 ## Optional: set environment variable AUGUSTUS_CONFIG_PATH
 
 If the environment variable AUGUSTUS_CONFIG_PATH is set, augustus and etraining will look there for the config directory that contains the configuration and parameter files, e.g. '~/augustus/config'. You may want to add this line to a startup script (like ~/.bashrc).
 
-```
-export AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/
-```
+    export AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/
 
 If this environment variable is not set, then the programs will look in the path ../config relative to the directory in which the executable lies. As a third alternative, you can specify this directory on the command line when you run augustus:
 --AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/
@@ -136,10 +128,10 @@ For further references see [docs/REFERENCES.md](docs/REFERENCES.md)
 # LICENSES
 
 All source code, i.e.
-  - the AUGUSTUS source code (src/*.cc, include/*.hh)
-  - the scripts (scripts/*)
-  - the auxiliary programs (auxprogs/)
-  - the tree-parser (src/scanner, src/parser)
-  - the unit tests (src/unittests)
+  - the AUGUSTUS source code (`src/*.cc`, `include/*.hh`)
+  - the scripts (`scripts/*`)
+  - the auxiliary programs (`auxprogs/`)
+  - the tree-parser (`src/scanner`, `src/parser`)
+  - the unit tests (`src/unittests`)
 
 is under the [Artistic License](src/LICENSE.TXT).