Linux安装sanger-pathogens-Roary

下载sanger-pathogens

$ git clone https://github.com/sanger-pathogens/Roary/tarball/masterhttps://github.com/sanger-pathogens/Roary/tarball/master

解压

$ tar zxvf sanger-pathogens-Roary-v3.12.0-17-gdb170bf.tar.gz

设置sanger-pathogens的环境变量

$export PATH=$PATH:~/sanger-pathogens-Roary-db170bf/bin/
$export PERL5LIB=$PERL5LIB:~/sanger-pathogens-Roary-db170bf/lib/

安装Perl依赖项

sudo cpanm  Array::Utils Bio::Perl Exception::Class File::Basename File::Copy File::Find::Rule File::Grep File::Path File::Slurper File::Spec File::Temp File::Which FindBin Getopt::Long Graph Graph::Writer::Dot List::Util Log::Log4perl Moose Moose::Role Text::CSV PerlIO::utf8_strict Devel::OverloadInfo Digest::MD5::File
# wget -c http://xrl.us/cpanm -O /usr/bin/cpanm
# chmod +x /usr/bin/cpanm

安装必要的依赖项

• bedtools cd-hit blast mcl GNUparallel prank mafft fasttree

• cd-hit安装

$wget https://github.com/weizhongli/cdhit/releases/download/V4.6.8/cd-hit-v4.6.8-2017-1208-source.tar.gz
$ tar -zxvf cd-hit-v4.6.8-2017-1208-source.tar.gz
$cd cd-hit-v4.6.8-2017-1208
$make
$cd cd-hit-auxtools/
$make
$export PATH=~/Software/cd-hit-v4.6.8-2017-1208/:$PATH

• blast安装

$  wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.6.0+-x64-linux.tar.gz
$ tar -zxvf ncbi-blast-2.9.0+-x64-linux.tar.gz
$ export PATH=~/Software/ncbi-blast-2.9.0+/bin/:$PATH
$ blastn -version
blastn: 2.9.0+
 Package: blast 2.9.0, build Mar 11 2019 15:20:05

• mcl安装

$ wget https://micans.org/mcl/src/mcl-12-068.tar.gz
$ tar xf mcl-12-068.tar.gz 
$ cd mcl-12-068
$ ./configure --prefix=~/Software/mcl/
$ make install
$ export PATH=~/Software/mcl/bin/:$PATH
$ mcl -h

• GNUparallel安装

$ wget http://ftp.gnu.org/gnu/parallel/parallel-20190622.tar.bz2
$ tar xf parallel-20190622.tar.bz2 
$ cd parallel-20190622
$ ./configure --prefix=~/parallel/20190622
$ make
$ make install
$ export PATH=~/Software/parallel/20190622/bin/:$PATH
$ which parallel

• prank安装

$ wget http://wasabiapp.org/download/prank/prank.linux64.140603.tgz
$ tar xf prank.linux64.140603.tgz
$ export PATH=~Software/prank/bin/:$PATH
$ which  prank
~/Software/prank/bin/prank

• mafft安装

# wget https://mafft.cbrc.jp/alignment/software/mafft-7.427-gcc_fc6.x86_64.rpm
# yum install mafft-7.427-gcc_fc6.x86_64.rpm
# which mafft
/usr/bin/mafft

• fasttree安装

$ wget http://www.microbesonline.org/fasttree/FastTree.c
$ gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm
$ export PATH=~/Software/fasttree/:$PATH

使用报错Error message: Cannot find the mcxdeblast executable, please ensure its in your PATH

解决网址

https://github.com/sanger-pathogens/Roary/issues/217

• 设置mcxdeblast到PATH

$ export PATH=~/Software/mcl-12-068/src/alien/oxygen/src/:$PATH