一、软件介绍：

BLASR：PacBio® 长读长对准器

开发语言：C++

源码地址：https://github.com/BioinformaticsArchive/blasr/archive/refs/heads/master.zip

二、安装步骤：

1、依赖szip安装:

cd /path/to/szip

wget https://distfiles.macports.org/szip/szip-2.1.1.tar.gz

tar xf szip-2.1.1.tar.gz

cd szip-2.1.1

./configure --prefix=/path/to/szip

make

make install

2、依赖hdf5安装：

cd /path/to/hdf5

wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz

tar xf hdf5-1.8.12.tar.gz

cd hdf5-1.8.12

./configure  --enable-cxx --enable-static=yes --enable-shared --prefix=/path/to/hdf5 --build=arm LDFLAGS="-L/path/to/szip/lib" CPPFLAGS="-I/path/to/szip/include"

make

make install

3、blasr安装

cd /path/to/blasr

wget https://github.com/BioinformaticsArchive/blasr/archive/refs/heads/master.zip

unzip master.zip

cd blasr-mater

sed -i "5c\HDF5INCLUDEDIR=/path/to/hdf5/include" common.mk

sed -i "6c\HDF5LIBDIR=/path/to/hdf5/lib" common.mk

sed -i "s/\-static//g" `grep -rnl "\-static"`

sed -i "13s/$/ -ldl/" common.mk

sed -i "33s/testIn/testIn.good()/g" ./common/data/hdf/HDFFile.h

sed -i "242c\ (unsigned int) curPrefix.tuple + 1 < (unsigned int) (this->lookupTableLength));" ./common/datastructures/suffixarray/SuffixArray.h

sed -i "2271s/cout <<//g" ./pbihdfutils/LoadPulses2.cpp 

sed -i "128s/ ==/.good() ==/" ./common/datastructures/alignmentset/SAMAlignment.h

make

三、运行验证：

cd /path/to/blasr/blasr-master/alignment/bin

./blasr -h