Antlr Install

 

Install Eclipse. Download ANTLR complete binaries jar that includes ANTLR v2. Extract to a temp directory. Copy the antlr-n.n folder to an appropriate permanent location, for example the same folder that Eclipse is installed in. Add ANTLR IDE update site to Eclipse. In Eclipse, click on Help and select Install New Software. Click Add button. This plugin is for ANTLR v4 grammars and includes ANTLR 4.9.1. It works with 2016.2-2020.3. It should work in other JetBrains IDEs. Comment grammar rule lines with meta-/ (1.7) save parse trees as svg/jpg/png; right click in parse tree view (1.9) grammar/comment folding (1.7) generates parser code; shortcut (ctrl-shift-G / meta-shift.

  1. Install antlr4 python3 runtime. Pip install antlr4-python3-runtime. Open command and run bin/antlr4.bat. You may need to compile the latest ANTLR4 and put it into bin, modify the bat file. You may also need to use the latest runtime, just copy the source to PythonDir Lib site-packages antlr4.
  2. I know setting up the Antlr on a windows machine is a little bit complicated even tough some expert users think that it is not! However, I'm going to create a full tutorial and will try to cover 'setting-up' and 'testing' the Antlr on a windows computer from A-Z.
  3. I installed the ANTLR plugin on IntelliJ 14 and was able to get it working. A couple little things made it harder than expected. The plugin settings are per ANTLR file (.g4) so highlight the.g4 file you want to generate, then right click to configure ANTLR. Otherwise, the ANTLR related context menus are greyed out.

Downloading SnpEff & SnpSift

SnpEff and SnpSift are bundled together.

Old versions here.

License

Install antlr nuget

SnpEff is open source, released as 'LGPLv3'.

System requirements

SnpEff requires that you have Java v1.8 or later installed (any modern operating system has it).

The amount of memory used can vary significantly depending on genome size and data analysis type you are doing.For large genomes, such as the human genome, you'll probably need at least 4Gb of memory.

Installing SnpEff

Install

Installing SnpEff is very easy, you just have to uncompress the ZIP file.

How to install using command line (unix systems)

It is better if you install SnpEff in snpEff directory in your home directory ($HOME/snpEff in unix systems).

Configuration

In most cases you DO NOT need to configure anything.

The only configuration file is snpEff.config.Most configuration parameters, are explained in the comments in the same config file, so I won't repeat the explanation here :-)

Usually you do NOT need to change the configuration.Some peoeple may need to change the location of the databases (data.dir parameter).By default, this parameter points to the data directory where you installed the tool (i.e. in unix systems, this is ./data).If you want to change this, you can edit the snpEff.config file and change the data_dir entry:

Downloading SnpEff databases

In order to perform annotations, SnpEff automatically downloads and installs genomic database.

Info

By default SnpEff automatically downloads and installs the database for you, so you don't need to do it manually.

Databases can be downloaded in three different ways:

  • The easiest way is to let SnpEff download and install databases automatically

  • You can pre-install databases manually using the SnpEff download command (once SnpEff is installed). E.g. to download the human genome database:

    Note: Current human genome version at the time of writing is GRCh38.76.

Install

Available databases

There are over 20,000 databases available.

A list of databases is available in snpEff.config file.You can also see all available databases by running the following command (once SnpEff has been installed):

Install antlr windows

Source code

Antlr Install

Install antlr visual studio

Getting the source

The source code is in GitHub (although we keep the binary distribution is at SourceForge).Here is the git command to check out the development version of the code:

Building from the source

Most libraries should be install using Maven, so you just need to run mvn command.

Pip Install Antlr

  • Java (JDK)
  • ANT
  • Maven

Brew Install Antlr

Some libraries are not available through maven, so you have to install them into via Maven manually (these libraries are in SnpEff/lib)

Install Antlr Windows

Once the libraries are installed, you can use make.sh to build the code

Antlr Install Ubuntu

Installing test cases

Install Antlr Nuget

Test cases require special 'test cases databases and genome', you can find them here: