https://github.com/PacificBiosciences/blasr/wiki/Step-by-step-blasr-installation-example
-
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
-
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
-
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
-
For optimized builds:
./configure.py CXXFLAGS=-O3 ...
-
For debug builds:
./configure.py CXXFLAGS=-g ...
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).
If you have built and installed blasr_libcpp elsewhere, then drop --sub
and do not run make build-submodule
.