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anuragraj edited this page Aug 16, 2023 · 8 revisions

PgxSAVy can be downloaded from https://github.com/anuragraj/PgxSAVy. The detailed usage and installation are given in this document.

This tool is written in Perl and tested on Windows, Linux and Mac platforms. Since Perl is platform independent and backwards compatible, it should run on most systems with Perl 5.10 or later which have the dependent modules.

A. Windows Install

  1. Install latest Perl for the compatible OS (32 or 64 bit) if not already there on the computer.

  2. In the case of ActivePerl, open the Perl package manager by typing ppm on the command-line. Add the suggested ppm Perl repositories from ppm first, so that all major packages become available. ppm guide can be found on ActiveState website. Install all dependencies one by one by searching/finding the module in the GUI or typing install MODULENAME on the command line. On DOS command line, type-

    C:\\Windows\\User\> ppm install MODULENAME

  3. In case of Strawberry Perl, install dependencies given in section "1.2. Dependencies" below using CPAN. Install all dependencies one by one by typing cpan MODULENAME on the command line. On DOS command line, type-

    C:\\Windows\\User\> cpan MODULENAME

B. Linux Install

  1. Linux and other UNIX based operating systems already have Perl installed.

  2. To check Perl, type on shell prompt.
    perl --v
    This command tells about the Perl version installed.

  3. Install the dependencies given in section "1.2. Dependencies" below from ppm or CPAN.

C. Macintosh Install

  1. gcc (preferably gcc-4.2) and make utilities are required to install all dependencies of PgxSAVy from CPAN. Please check whether gcc and make are installed on your MAC system by following steps.

    a) Open a terminal.

    b) Type a command which GCC. If a path displaying GCC location is returned means GCC is installed, else GCC is not installed.

    c) Type a command which make. If a path displaying make location is returned make is installed else you need to install make utility.

    In case gcc or make is not installed, download XCode from the MAC app store and install. Older versions of MAC OS need a compatible Xcode version which can be found among the software distributed with the machine.

    Repeat the step (a), (b) and (c) to make sure if gcc and make have been installed successfully.

  2. Root user login is required to install PgxSAVy dependencies through CPAN. By default, root user login is disabled in MAC OS. To know how to enable root login please follow the link http://support.apple.com/kb/ht1528.

  3. Once the steps 1 and 2 are completed, go through sub-steps i. to iii. one by one to install all the required modules/dependencies for PgxSAVy.

    i. Open the terminal and login by root user id.

    ii. Type CPAN and press enter, wait until it loads properly.

    iii. Type install Statistics::Zed and press enter.

Note: To check whether a module was installed correctly, the user needs to check the message install -- OK at the end of the CPAN terminal after each module installation. Once the modules are installed, the next section on 1.2 Dependencies can be ignored.

Bioannotation variant database download

Varinat database from Uniprot is required to be downloaded from followink link:
Link: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/variants/homo_sapiens_variation.txt.gz

After downloading unzip the file and copy it to PgxSAVy directory.

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