Set up Squirls
Squirls is a desktop Java application that requires several external files to run. This document explains how to download these files and prepare to run Squirls.
Note
Squirls is written with Java version 11 and will run and compile under Java 11+.
Squirls downloadable resources
There are several external files that must be downloaded prior running Squirls.
Prebuilt Squirls executable
To download the prebuilt Squirls JAR file, go to the Releases section on the Squirls GitHub page and download the latest precompiled version of Squirls.
Squirls database files
Squirls database files are available for download from the following locations:
Version |
Genome build |
URL |
Size |
|---|---|---|---|
2103 |
hg19/GRCh37 |
~10.5 GB for download, ~15 GB unpacked |
|
2103 |
hg38/GRCh38 |
~11.1 GB for download, ~16.5 GB unpacked |
|
2203 |
hg19/GRCh37 |
~9.5 GB for download, ~11.9 GB unpacked |
|
2203 |
hg38/GRCh38 |
~9.9 GB for download, ~12.2 GB unpacked |
Note
The 2103 works with Squirls v1.0.0, the 2203 works with Squirls v2.0.0.
Use curl or wget utilities to download the files from command line:
$ wget https://storage.googleapis.com/squirls/2203_hg38.zip
or
$ curl --output 2203_hg38.zip https://storage.googleapis.com/squirls/2203_hg38.zip
Alternatively, use a GUI FTP client such as FileZilla.
After the download, unzip the archive(s) content into a folder and note the folder path.
Build Squirls from source
As an alternative to using prebuilt Squirls JAR file, the Squirls JAR file can also be built from Java sources.
Run the following commands to download Squirls source code from GitHub repository and to build Squirls JAR file:
$ git clone https://github.com/TheJacksonLaboratory/Squirls
$ cd Squirls
$ ./mvnw package
Note
To build Squirls from sources, JDK 11 or better must be available in the environment
After the successful build, the JAR file is located at squirls-cli/target/squirls-cli-2.0.0.jar.
To verify that the building process went well, run:
$ java -jar squirls-cli/target/squirls-cli-2.0.0.jar --help