Table of Contents

blasr

BLASR: The PacBio® long read aligner.

Information

Usage

See versions of blasr which are available: 

$ module avail blasr

Load one version into your environment: 

$ module load blasr/smrtanalysis-4.0.0

Installation

Notes from the sysadmin during installation: 

$ cd /tmp
$ git clone https://github.com/PacificBiosciences/blasr.git blasr
$ cd blasr
$ git checkout smrtanalysis-4.0.0
$ git submodule update --init
$ scl enable devtoolset-4 bash
$ ./configure.py CXXFLAGS=-O3 --shared --sub --no-pbbam HDF5_INCLUDE=/export/apps/hdf5/1.8.19/include HDF5_LIB=/export/apps/hdf5/1.8.19/lib
$ make configure-submodule
$ make build-submodule
$ make -j4
$ sudo mkdir -p /export/apps/blasr/smrtanalysis-4.0.0
$ sudo chown aorth /export/apps/blasr/smrtanalysis-4.0.0
$ find . -iname "*.o" -delete
$ cp -r blasr libcpp utils /export/apps/blasr/smrtanalysis-4.0.0

Note: I installed the smartanalysis-4.0.0 tag because the master branch has switched to a cmake-based build system and is still not working properly (perhaps just on old CentOS with lots of manually compiled external dependencies).