Maven install source codes from zip
- #Maven install source codes from zip how to#
- #Maven install source codes from zip pro#
- #Maven install source codes from zip code#
Some libraries are not available through maven, so you have to install them into via Maven manually (these libraries are in SnpEff/lib) # Go to 'lib' dir Most libraries should be install using Maven, so you just need to run mvn command. Here is the git command to check out the development version of the code: # Get SnpEff
#Maven install source codes from zip code#
The source code is in GitHub (although we keep the binary distribution is at SourceForge). You can also see all available databases by running the following command (once SnpEff has been installed): java -jar snpEff.jar databases There are over 20,000 databases available.Ī list of databases is available in nfig file. Note: Current human genome version at the time of writing is GRCh38.76. to download the human genome database: java -jar snpEff.jar download GRCh38.76 You can pre-install databases manually using the SnpEff download command (once SnpEff is installed).Į.g. The easiest way is to let SnpEff download and install databases automatically.
#Maven install source codes from zip pro#
Instructions on Git use can be found in the online book Pro Git. Instructions on Subversion use can be found in the online book Version Control with Subversion. In order to perform annotations, SnpEff automatically downloads and installs genomic database.īy default SnpEff automatically downloads and installs the database for you, so you don't need to do it manually.ĭatabases can be downloaded in three different ways: Maven projects use Git or Subversion to manage their source code: decisions to stay with Subversion or move to Git are tracked on Maven's Wiki. # Also, a non-absolute path will be relative to config's file dir # You can use tilde ('~') as first character to refer to your home directory.
# E.g.: Information for 'hg19' is stored in data_dir/hg19/ If you want to change this, you can edit the nfig file and change the data_dir entry: #. Some peoeple may need to change the location of the databases ( data.dir parameter).īy default, this parameter points to the data directory where you installed the tool (i.e. Usually you do NOT need to change the configuration. Most configuration parameters, are explained in the comments in the same config file, so I won't repeat the explanation here :-) In most cases you DO NOT need to configure anything. It is better if you install SnpEff in snpEff directory in your home directory ( $HOME/snpEff in unix systems).
#Maven install source codes from zip how to#
How to install using command line (unix systems) Installing SnpEff is very easy, you just have to uncompress the ZIP file. The amount of memory used can vary significantly depending on genome size and data analysis type you are doing.įor large genomes, such as the human genome, you'll probably need at least 4Gb of memory. SnpEff requires that you have Java v1.8 or later installed (any modern operating system has it). SnpEff is open source, released as "LGPLv3". Each project has a single pom.xml file, and each pom.xml file has a project element and three mandatory fields: groupId, artifactId, and version. Open the pom.xml file and review the code. Regulatory and Non-codingĭownload and install Downloading SnpEff & SnpSift By default, Maven adds the App.java source file and the AppTest.java test file to the default directory structure.