A collection of modules and scripts for processing and analysing large quantities of sequencing data.
This readme is inaccurate and requires updating
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.
For example:
perldoc VertRes::Utils::Sam
An overview, guides and how-tos are available on the GitHub wiki.
vr-codebase has the following dependencies:
- samtools
- Filesys::DfPortable
- Filesys::DiskUsage
- File::Fetch
- File::Rsync
- File::Temp
- Net::FTP::Robust
- Time::Format
- IO::Capture::Stderr
- Math::Random
- Bio::Assembly::Improvement
- Bio::AutomatedAnnotation
- Bio::RNASeq
- Bio::VertRes::Permissions
- GATK
- picard
- beagle
For samtools you need the source version 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 recommended that you set PERL_INLINE_DIRECTORY to ~/.Inline
Some dependencies need environment variables setup (using setenv in csh or export in bash). The following table shows the name of the software, the environment variable you need to set, and the value you should set it to.
| Software | Environment variable | Value |
|---|---|---|
| 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 |
Details for the installation are provided below. If you encounter an issue when installing vr-codebase please contact your local system administrator. If you encounter a bug please email us at path-help@sanger.ac.uk.
To build vr-codebase:
perl Build.PL
If this says you have "ERRORS/WARNINGS FOUND IN PREREQUISITES", install missing prerequisites from CPAN:
./Build installdeps
To test the code prior to use:
perl Build.PL
./Build test
To install:
./Build install
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.
Tracking of meta-data, required for many of our pipelines, occurs in a mysql database. We use 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.
Usage: run-pipeline [OPTIONS]
Options:
-c, --config <file> The file containing the projects.
-d, --done List of completed jobs (i.e. jobs with the status 'done')
-f, --failed List jobs which failed repeatedly (i.e. jobs with the status 'failed').
-l, --logfile <file> Where to put logging stuff.
-L, --lockfile <file> Run only if there is no other process running.
-m, --max-lsf-jobs <int> Allow at most this many LSF jobs in queue.
-o, --once Run all jobs only once and then exit.
-s, --sleep-time <int> Check the projects every N minutes.
-t, --todo List jobs which should be run (i.e. jobs with the status 0,1,2).
-a, --dont_check_load Dont halt script if the load is higher than the number of CPUs.
-b, --same_database_for_all All config files refer to the same DB so reuse connection.
-v, --verbose Be verbose. (Given twice increases the verbosity level.)
For more information, please see the GitHub wiki.
Vr-codebase is free software, licensed under GPLv3