Compiling BLASR

BLASR is Pacific Biosciences' long read aligner.[1]

Installed Version

Version 1.3.1 is installed on Proteus. Use the module:

pacbio/blasr/gcc/20150513

Check the version by doing:

[juser@proteusa01 ~]$ blasr -version

Also installed are the various utilities, e.g. alchemy, evolve, samFilter, etc.

Known Bug

There is an existing bug with multithreaded blasr[2]: running multithreaded blasr causes it to crash and dump core. There is no comment by the authors on that bug, though it has been assigned. The workaround is to run it single-threaded.

General Notes

We use the refactored code, currently (2015-05-13) hosted at https://github.com/ylipacbio/refactored_blasr_II but which will soon replace the main git repository
BLASR depends on HDF5 1.8

Environment

Currently Loaded Modulefiles: 1) shared 3) gcc/4.8.1 5) szip/gcc/2.1 2) proteus 4) sge/univa 6) hdf5_18/gcc/1.8.14-serial

Check Out Source

Clone the repository:

[juser@proteusa01 myresearchGrp]$ mkdir src ; cd src [juser@proteusa01 myresearchGrp]$ git clone git@github.com:ylipacbio/refactored_blasr_II.git --recursive

Modify top level Makefile

Edit the Makefile at the top level to remove the "static" flag.

ifneq ($(OS), Darwin)
    LIBS += -lrt
    ### do not use "-static"
    #STATIC := -static
    STATIC :=
else
    STATIC :=
endif

Modify tools/Makefile

The Makefile in the tools subdirectory contains rules which use the "-static" flag directly, rather than via the $(STATIC) macro. Delete every instance of "-static".

References

[1] BLASR GitHub project page

[2] BLASR issue #158