Download and Installation
1. Go to SourceForge.net to download our Perl scripts for the VariantClassifier:
To download the latest version of the VariantClassifier, go to our SourceForge project page:
You should see a large green button that is labeled "Download Now!". Follow the Sourceforge instructions if you are having problems with the download. (You may need to try a "direct link" or another "mirror".) Save the compressed file where you want to install the software. You will see a file named: "variant_classifier_<release date>.gz". Where the <release date> is the date the current files have been packaged together for a public release.
2. Uncompress the VariantClassifier source:
In your Unix command prompt do the following:
tar -xvf variant_classifier_<release date>.gz
This will create a directory named SNPClassifier, which contains the source code, documentation and examples.
3. Install Ensembl API (if you want to plan to use Ensembl annotation, if not, skip.):
If you plan on using the Extracting_Coding_Info.pl or Show_Latest_Databases.pl script to take advantage of annotation already present in Ensembl, you will need to download the Ensembl Perl API. It is necessary to go to the Ensemble web site to download the Perl APIs. We recommended you download all three API's. This will save you time in the future if you need them, and also prevent the possibility of incompatible versions or other unexpected dependencies between them. See http://www.ensembl.org/info/data/api.html and http://www.ensembl.org/info/docs/api/api_installation.html for in depth information and complete installation instruction, respectively. Unfortunately, we do not have the resources to assist you if you encounter installation problems with the API, however Ensembl does offer a responsive help service on their databases and software.
4. You're done, trying running your scripts.
All scripts in the VariantClassifier package provide usage information when the script is invoked without any parameters. If you do not have modules properly installed, you will see error messages immediately. Frequently this will be a PERL5LIB environmental variable problem, or the inability of the script to find your Perl executable. (See the Frequently Asked Questions). Unfortunately, we do not have the resources to assist with all Perl problems, but if you encounter a problem or a solution to one, that you believe most other users will encounter, please send me an e-mail, kli at jcvi.org, and we will include a solution in the FAQ page, and acknowledge you if you wish.