AUGUSTUS的普通用户安装

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make[2]: Entering directory `$HOME/software/augustus-3.3.1/auxprogs/bam2hints'
make[2]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
g++ -Wall -O2    -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools
bam2hints.cc:16:10: fatal error: api/BamReader.h: No such file or directory
 #include <api/BamReader.h>
          ^~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [bam2hints.o] Error 1
make[2]: Leaving directory `$HOME/software/augustus-3.3.1/auxprogs/bam2hints'
make[1]: *** [all] Error 2
make[1]: Leaving directory `$HOME/software/augustus-3.3.1/auxprogs'
make: *** [all] Error 2

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sudo apt-get install bamtools libbamtools-dev

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wget https://github.com/pezmaster31/bamtools/archive/v2.4.1.tar.gz -O bamtools-2.4.1.tar.gz
tar zxf bamtools-2.4.1.tar.gz
cd bamtools-2.4.1
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=/your/path/to/bamtools ..
make
make install

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$ ~/opt/bamtools-2.4.1/bin/bamtools
$HOME/opt/bamtools-2.4.1/bin/bamtools: error while                                                 loading shared libraries: libbamtools.so.2.4.1: cannot open shared                                                 object file: No such file or directory

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First, go to the “./auxprogs/bam2hints” directory and make the following changes for the Makefile:

Add:
BAMTOOLS = $HOME/opt/bamtools-2.4.1

Replace:
INCLUDES = /usr/include/bamtools
By:
INCLUDES = $(BAMTOOLS)/include

Replace:
LIBS = -lbamtools -lz
By:
LIBS = $(BAMTOOLS)/lib/bamtools/libbamtools.a -lz

Then, go to the “augustus-3.2.3/auxprogs/filterBam/src” directory and make the following changes for the Makefile:
Replace:

BAMTOOLS = /usr/include/bamtools
By:
BAMTOOLS = $HOME/opt/bamtools-2.4.1

Replace:
INCLUDES = -I$(BAMTOOLS) -Iheaders -I./bamtools
By:
INCLUDES = -I$(BAMTOOLS)/include -Iheaders -I./bamtools

Replace:
LIBS = -lbamtools -lz
By:
LIBS = $(BAMTOOLS)/lib64/libbamtools.a -lz

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./configure --prefix=/where/to/install
make
make install

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# SAMTOOLS=$(TOOLDIR)/samtools/
SAMTOOLS=$HOME/software/samtools-1.9

#HTSLIB=$(TOOLDIR)/htslib/
HTSLIB=$HOME/software/htslib-1.9

# BCFTOOLS=$(TOOLDIR)/bcftools/
BCFTOOLS=$HOME/software/bcftools-1.9

# TABIX=$(TOOLDIR)/tabix/
TABIX=$HOME/software/htslib-1.9

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make[2]: Entering directory `$HOME/software/augustus-3.3.1/auxprogs/bam2wig'
make[2]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
gcc -Wall -O2 -I$HOME/opt/samtools-1.8/ -I. -I$HOME/opt/htslib-1.9/ -I$HOME/opt/bcftools-1.9/ -I$HOME/opt/htslib-1.9/ -c bam2wig.c -o bam2wig.o
bam2wig.c:18:10: fatal error: sam.h: No such file or directory
 #include "sam.h"
          ^~~~~~~
compilation terminated.

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hfile_s3.c:(.text+0x8d7): undefined reference to `EVP_sha1'
hfile_s3.c:(.text+0x8fd): undefined reference to `HMAC'
collect2: error: ld returned 1 exit status

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hfile_libcurl.c:(.text+0x12aa): undefined reference to `curl_global_cleanup'
collect2: error: ld returned 1 exit status

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##清除之前未成功编译的中间文件，回复初始状态
make clean
##多线程编译缩短时间
make -j 8
echo 'PATH=$PATH:~/opt/augustus/bin:~/opt/augustus/scripts' >> ~/.bashrc
##可选步骤，手动设置配置文件夹的路径。如未设置，默认会搜寻可执行文件相对路径../config中的文件。
echo 'AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/' >> ~/.bashrc