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This repository contains the internally-developed software used by the Vertebrate Resequencing group at the Sanger Institute. It comprises mostly self-documented Perl code. There are both scripts and modules within subfolders. Each module has its own POD, so please use perldoc or similar for further help. Eg: $ perldoc VertRes::Utils::Sam An overview, guides and how-tos are available on the github wiki: https://github.com/VertebrateResequencing/vr-codebase/wiki INSTALLATION ------------ You will need the source version of samtools compiled with -fPIC and -m64 in the CFLAGS, and the environment variable SAMTOOLs pointing to that source directory (which should now contain bam.h and libbam.a). It is also recommended that you set PERL_INLINE_DIRECTORY to ~/.Inline $ perl Build.PL If this says you have "ERRORS/WARNINGS FOUND IN PREREQUISITES" try: $ ./Build installdeps to install missing prerequisites from CPAN. To test the code prior to use: $ perl Build.PL $ ./Build test To install: $ ./Build install (or just point your PERL5LIB to the modules subdirectory, and include the scripts subdirectory in your PATH) EXTERNAL SOFTWARE ----------------- Most likely some of the tests will fail due to you not having certain external software installed. If you don't plan on making use of that software, just ignore it when a test script for that software fails. Some software also need environment variables setup (using setenv in csh or export in bash). The following list shows the name of the software, the environment variable you need to set, and the value you should set it to, separated by commas. samtools,SAMTOOLS,/path/to/samtools/source_directory GATK,GATK,/path/to/gatk_jar_files GATK,STING_DIR,/path/to/gatk_source_code_checkout GATK,GATK_RESOURCES,/path/to/resource_files_like_reference_etc picard,PICARD,/path/to/picard_jar_files beagle,BEAGLE,/path/to/beagle_install_directory eg. to have picard work properly in our pipelines you might do: setenv PICARD /path/to/picard_jar_files or export PICARD=/path/to/picard_jar_files depending on what shell you are using. VRTRACK DATABASE ---------------- Tracking of meta-data, required for many of our pipelines, occurs in a mysql database. We use more environement variables to define how to access the mysql database: VRTRACK_HOST VRTRACK_PORT VRTRACK_RO_USER VRTRACK_RW_USER VRTRACK_PASSWORD The RW user you setup should have permissions to create and alter databases. We assume that the RO user does not require a password.