Augustus-3.3.3安装

git clone https://github.com/Gaius-Augustus/Augustus.git

cd Augustus

1.bam2hints compile error

vim auxprogs/bam2hints/Makefile

# Variable definition
BAMTOOLS=/home/software/bamtools
#INCLUDES = /usr/include/bamtools
INCLUDES = -I${BAMTOOLS}/include/bamtools
#LIBS = -lbamtools -lz
LIBS = ${BAMTOOLS}/lib64/libbamtools.a -lz

2.filterBam compile error

vim auxprogs/filterBam/src/Makefile

#BAMTOOLS = /usr/include/bamtools
BAMTOOLS = /home/software/bamtools
#INCLUDES = -I$(BAMTOOLS) -Iheaders -I./bamtools
INCLUDES = -I$(BAMTOOLS)/include/bamtools -Iheaders -I./bamtools
#LIBS = -lbamtools -lz
LIBS = ${BAMTOOLS}/lib64/libbamtools.a -lz

3.bam2wig compile error

mkdir samtools

  git clone https://github.com/samtools/htslib.git
  cd htslib
  autoheader
  autoconf
  ./configure --prefix=$(pwd)
  make
  make install
  cd ..
  
  git clone https://github.com/samtools/bcftools.git
  cd bcftools
  autoheader
  autoconf
  ./configure --prefix=$(pwd)
  make
  make install
  cd ..

 git clone https://github.com/samtools/samtools.git
  cd samtools
  autoheader
  autoconf -Wno-syntax
  ./configure --prefix=$(pwd)
  make
  make install
  cd ..

bcftools  bcftools-1.11.tar.bz2  htslib  htslib-1.11.tar.bz2  samtools  samtools-1.11.tar.bz2

vim auxprogs/bam2wig/Makefile
TOOLDIR=/home/software/samtools
ifndef TOOLDIR
        TOOLDIR=$(HOME)/tools
# replace with your own parent directory of samtools, htslib, bcftools
# if TOOLDIR is not specified as environment variable
endif

make
...
...
make[2]: Leaving directory '/home/software/Augustus/auxprogs/bam2wig'
make[1]: Leaving directory '/home/software/Augustus/auxprogs'