Installation¶
Quick start¶
Basically, download ASCIIGenome-X.Y.Z.zip
from releases,
unzip, copy ASCIIGenome
and 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/
With conda¶
ASCIIGenome is available as a bioconda package and it can be installed with the conda package manager:
conda install -c bioconda asciigenome
With Homebrew¶
ASCIIGenome can also be installed through brew / Linux Brew, although it is still not an official package:
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
script ASCIIGenome
and the jar file ASCIIGenome.jar
in the same directory in your PATH
and execute with:
ASCIIGenome [options]
Note
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 /usr/local/bin/
, e.g.:
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 $HOME/bin
(e.g. /home/myName/bin
or /Users/myName/bin
or short ~/bin
). e.g.:
cp ASCIIGenome.jar ~/bin/
cp ASCIIGenome ~/bin/
If ~/bin
does not exist or is not on your PATH create it with:
mkdir ~/bin/
And to add to it to your PATH edit your profile file to add the new
directory. E.g. edit ~/.bash_profile
to:
PATH=/home/myName/bin:$PATH
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 -nf
option.
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 build/libs/ASCIIGenome.jar
.
The -x test
option builds the code without running the tests.