ASCIIGenome-X.Y.Z.zip from releases,
ASCIIGenome.jar to a directory of your liking and that’s it.
For example, in the commands below replace version number with the latest from releases:
wget https://github.com/dariober/ASCIIGenome/releases/download/vX.Y.Z/ASCIIGenome-x.y.z.zip unzip ASCIIGenome-x.y.z.zip cd ASCIIGenome-x.y.z/ chmod a+x ASCIIGenome cp ASCIIGenome.jar /usr/local/bin/ # Or else in your PATH e.g. ~/bin/ cp ASCIIGenome /usr/local/bin/ # Or else in your PATH e.g. ~/bin/
ASCIIGenome is available as a bioconda package and it can be installed with the conda package manager:
conda install -c bioconda asciigenome
brew install https://raw.githubusercontent.com/dariober/ASCIIGenome/master/install/brew/asciigenome.rb
A little more detail¶
ASCIIGenome.jar requires Java 1.8+ and this should be the only requirement. There is virtually no installation needed as
ASCIIGenome is pure Java and should work on most (all?) platforms. Download the zip file
ASCIIGenome-x.x.x.zip from releases, unzip it and execute the jar file with:
java -jar /path/to/ASCIIGenome.jar --help
To avoid typing
java -jar ... every time, you can put both the helper
ASCIIGenome and the jar file
ASCIIGenome.jar in the same directory in your
PATH and execute with:
This part below has nothing to do with ASCIIGenome specifically. These are just general instructions to add executable files to your PATH.
For Unix users: If you have administrator rights and you want to make ASCIIGenome available to all users,
a popular choice of installation directory is
cp ASCIIGenome.jar /usr/local/bin/ cp ASCIIGenome /usr/local/bin/
If you don’t have administrator rights (i.e. you get a
Permission denied error) you can instead copy to a directory that you have on your
PATH and where you have permission to write. A popular user directory for executable files is
/Users/myName/bin or short
cp ASCIIGenome.jar ~/bin/ cp ASCIIGenome ~/bin/
~/bin does not exist or is not on your PATH create it with:
And to add to it to your PATH edit your profile file to add the new
directory. E.g. edit
Then reload the profile file or log off and log back in to make the changes effective.
Note the helper is a bash script. To set the amount of memory available to java use the
-Xmx option as e.g.
java -Xmx1500m -jar ....
If for some reason the text formatting misbehave, disable it with the
Compiling the source code¶
From version 1.13 ASCIIGenome is built using the gradle build tool. If you want to edit the source code and re-compile it to an executable jar, all you need to do is:
# Get source git clone https://github.com/dariober/ASCIIGenome.git cd ASCIIGenome ./gradlew clean ./gradlew build -x test
The executable jar file will be in
-x test option builds the code without running the tests.