Birdsuite: Install

Limitations

  • Currently, this Birdsuite release only runs on 32- or 64-bit Linux systems, although it may be possible to make it work on other systems, particularly if you have Matlab for the target system.
  • Currently, Birdsuite metadata exists only for Affymetrix Genome-Wide Human SNP Array 6.0.
  • Some files are not distributed by Broad Institute, and must be obtained from other parties.

Prerequisites

Prerequisites for building executables from sources

Files to download

The following files are available for download:
FileDescription
birdsuite_executables_<version>.tgz Scripts and executables that are already built for Linux
birdsuite_metadata_<version>.tgz Metadata required by Birdsuite
MCRInstaller.75.glnxa64.bin.gz Matlab 7.5 compiled runtime for 64-bit Linux
MCRInstaller.75.glnx86.bin.gz Matlab 7.5 compiled runtime for 32-bit Linux
birdsuite_inputs_<version>.tgz Test inputs for birdsuite (optional)
birdsuite_outputs_<version>.tgz Output from test inputs (optional)
birdsuite_sources_<version>.tgz Source code (optional)

Click here to download files.

Installation

  1. Create a directory where all the Birdsuite executables will go. We'll call this EXEDIR.
  2. Unpack birdsuite_executables_<version>.tgz into EXEDIR.
  3. Install python packages. Please follow (CLICK THIS LINK) python install documentation
  4. For 64-bit, copy (or symlink) the 64-bit version of apt-probeset-summarize from Affymetrix Power Tools into EXEDIR, with the name apt-probeset-summarize.64 . For 32-bit, copy or symlink the 32-bit version of apt-probeset-summarize into EXEDIR, with the name apt-probeset-summarize . Note that you may do both of the above to run on both 32- and 64-bit systems.
  5. Run the following commands:

    R CMD INSTALL -l EXEDIR EXEDIR/broadgap.utils_<version>.tar.gz
    R CMD INSTALL -l EXEDIR EXEDIR/broadgap.cnputils_<version>.tar.gz
    R CMD INSTALL -l EXEDIR EXEDIR/broadgap.canary_<version>.tar.gz
  6. Install Matlab compiled runtime:
    • For 64-bit:
      1. Download MCRInstaller.75.glnxa64.bin.gz and decompress into temporary directory.
      2. Run the following command:
        MCRInstaller.75.glnxa64.bin -console
      3. When prompted for a directory into which to install MCR, reply with EXEDIR/MCR75_glnxa64
      4. MCRInstaller.75.glnxa64.bin may be deleted after installation is complete.
    • For 32-bit:
      1. Download MCRInstaller.75.glnx86.bin.gz and decompress into temporary directory.
      2. Run the following command:
        MCRInstaller.75.glnx86.bin -console
      3. When prompted for a directory into which to install MCR, reply with EXEDIR/MCR75_glnx86
      4. MCRInstaller.75.glnx86.bin may be deleted after installation is complete.
    Note that you may do both of the above to run on both 32- and 64-bit systems.
  7. Create a directory where all the Birdsuite metadata will go. We'll call this METADATADIR.
  8. Unpack birdsuite_metadata_<version>.tgz into METADATADIR.
  9. Copy the following files from the Affymetrix library bundle (genomewidesnp6_libraryfile.zip) into METADATADIR: GenomeWideSNP_6.Full.cdf, GenomeWideSNP_6.specialSNPs. For 5.0 chip, copy the analogous files.
  10. Edit EXEDIR/birdsuite.sh, and add the following arguments to the java command line: --exeDir=EXEDIR --metadataDir=METADATADIR
If you wish to use the birdsuite_qc.py script, which makes running mini-DM and gender calling easier, follow these additional installation steps.
  1. Copy or symlink GenomeWideSNP_6.cdf into METADATADIR. For 5.0 chip, copy the analogous files.
  2. Copy or symlink apt-geno-qc (from APT) into EXEDIR.

Testing

  1. Create a directory (TESTDIR) and unpack birdsuite_inputs_<version>.tgz there.
  2. cd to TESTDIR.
  3. Run the following command:

    EXEDIR/birdsuite.sh --basename=test --chipType=GenomeWideSNP_6 --outputDir=output --genderFile=test.gender --celFiles=test.cels --noLsf --apt_probeset_summarize.force
  4. Create a directory (EXPECTEDDIR) and unpack birdsuite_outputs_<version>.tgz there.
  5. Compare the files test.birdseed_calls, test.birdseed_confs, test.canary_calls, test.canary_confs, test.larry_bird_calls, test.larry_bird_confs in EXPECTEDDIR and TESTDIR/output. They should be identical.