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README.INSTALL.md

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Installation

See a step by step Blasr installation example on Blasr wiki page

    https://github.com/PacificBiosciences/blasr/wiki/Step-by-step-blasr-installation-example

Download source code

  • To pull this project from git hub to your local system:

      git clone git://github.com/PacificBiosciences/blasr.git blasr

  • To sync your code with the latest git code base:

      git pull --rebase origin master && git submodule update --init

  • To update the submodule:

      make update-submodule

Requirements

  • To configure:

      ./configure.py --shared --sub --no-pbbam

  • or with HDF5 directories (and note that HDF5_LIB is a directory here):

      ./configure.py --shared --sub --no-pbbam HDF5_INCLUDE=... HDF5_LIB=...

To build BLASR, you must have hdf 1.8.12 or above installed and configured with c++ support (you should have the library libhdf5_cpp.a). If you are intalling the entire PacBio secondary analysis software suite, appropriate hdf libraries are already distributed and no configuration is necessary. Otherwise, it is necessary to point two environment variables:

  • HDF5_INCLUDE, which points to directory of the HDF5 headers (e.g., hdf5.h)

  • HDF5_LIB, which points to the HDF5 library directory (e.g., hdf5*.a, and hdf5*.so)

You may pass arguments to configure.py as above, or you may export them from command line:

    export HDF5_INC=path_to_your_hdf5_include && export HDF5_LIB=path_to_your_hdf5_lib

  • To configure submodule:

    make configure-submodule

Build

  • To make the 'libcpp' libraries:

      make build-submodule

  • To make 'blasr' only:

      make blasr

  • To compile all tools, including blasr, pls2fasta, loadPulses, sawriter:

      make
    • Frequently used executables will be under utils.

  • To test (with cram installed):

      #make cramtests
  make cramfast
  ## Currently:
  ## Ran 22 tests, 0 skipped, 4 failed.

  • To clean all compiled tools and lib:

      make cleanall

  • To clean compiled tools without cleaning lib:

      make clean

  make blasr
  ./blasr

CXXFLAGS

  • For optimized builds:

    ./configure.py CXXFLAGS=-O3 ...

  • For debug builds:

    ./configure.py CXXFLAGS=-g ...

Other issues

Static binaries

If you want static binaries, drop --shared when you run configure.py. In that case, you might need to pass -lsz to make, if you built HDF5 with szlib support (--with-szlib).

    ./configure.py --with-szlib ...

See our issues.

If you have macosx (Darwin), then you almost certainly want non-static binaries (--shared).

blasr_libcpp

If you have built and installed blasr_libcpp elsewhere, then drop --sub and do not run make build-submodule.