在該頁(yè)面登記后會(huì)彈出下載鏈接:http://weatherby.genetics.utah.edu/cgi-bin/registration/maker_license.cgi
1.安裝perl包
requires:
! Bit::Vector is not installed
! IO::All is not installed
! Inline::C is not installed
! Perl::Unsafe::Signals is not installed
! Want is not installed
! forks is not installed
! forks::shared is not installed
recommends:
* DBD::Pg is not installed
使用conda批量安裝,將上述Perl包名全部寫入requirements.txt文件中
$ vi requirements.txt
perl-inline-c
perl-perl-unsafe-signals
perl-want
perl-forks
perl-dbd-pg
conda install -c bioconda --file=requirements.txt
2.配置MPI
在OpenMPI官網(wǎng)(https://www.open-mpi.org/)下載合適的opemMPI版本
tar zvxf openmpi-4.1.2.tar.gz
mkdir MPI
cd openmpi-4.1.2
./configure --prefix=/path/MPI/ #寫絕對(duì)路徑
3.安裝依賴軟件
3.1 安裝WuBlast或NCBI-BLAST
安裝NCBI-BLAST 2.2.X或更高的版本
下載地址:Index of /blast/executables/blast+/LATEST (nih.gov)
解壓并安裝
vi ~/.bashrc
export PATH=/usr/local/ncbi-blast:$PATH
3.2 安裝SNAP
下載地址:http://korflab.ucdavis.edu/software.html
解壓并安裝
vi ~/.bashrc
export ZOE=/usr/local/snap/Zoe:$PATH
export PATH=/usr/local/snap:$PATH
3.3 安裝RepeatMasker
下載地址:Download Page (repeatmasker.org)
基因組重復(fù)序列檢測(cè):RepeatMasker的安裝及使用 - 簡(jiǎn)書 (jianshu.com)
Tips:
需要安裝TRF、如果沒(méi)有安裝WuBlast則還需安裝RMBlast
在http://www.girinst.org下載Repeat Masker版本的Repbase repeat database, 解壓在RepeatMasker/Libraries目錄下,再執(zhí)行編譯产上,因?yàn)閏onfigure第一步就是檢查數(shù)據(jù)庫(kù)
tar zvxf RepeatMasker-4.1.2-p1.tar.gz
cd RepeatMasker
#準(zhǔn)備數(shù)據(jù)庫(kù)
wget https://www.dfam.org/releases/Dfam_3.2/families/Dfam.h5.gz
gunzip Dfam.h5.gz
mv Dfam.h5 /path/RepeatMasker/Libraries
cp RepBaseRepeatMaskerEdition-20181026.tar.gz /path/RepeatMasker/
cd /path/RepeatMasker
tar xzvf RepBaseRepeatMaskerEdition-20181026.tar
rm RepBaseRepeatMaskerEdition-20181026.tar
perl ./configure
vi ~/.bashrc
export PATH=/path/RepeatMasker:$PATH
export LIBDIR=/path/RepeatMasker/Libraries:$LIBDIR
3.4 安裝Exonerate 2.2
下載地址: http://www.ebi.ac.uk/~guy/exonerate
解壓安裝包
./configure -prefix=/usr/local/exonerate
make && make install
vi ~/.bashrc
export PATH=/usr/local/exonerate/bin:$PATH
3.5 安裝AUGUSTUS
下載地址:http://bioinf.uni-greifswald.de/augustus/
Augustus安裝教程 - 簡(jiǎn)書 (jianshu.com)
3.5 安裝MAKER
tar zvxf maker-3.01.04.tgz
cd ./maker/src
perl Build.PL
./Build install
~/.bashrc中必須包含:
export ZOE=where_snap_is/Zoe:$PATH
export AUGUSTUS_CONFIG_PATH=where_augustus_is/config:$PATH
vi ~/.bashrc
export PATH=/usr/local/maker/bin:$PATH
運(yùn)行:
maker [options] <maker_opts> <maker_bopts> <maker_exe>
參考文章:使用Anconda批量安裝Pythony庫(kù)(依賴包)的方法_閆小亙的博客-CSDN博客_conda 批量安裝
無(wú)sudo/root的情況下怎么安裝OpenMPI_熱愛(ài)可抵漫長(zhǎng)歲月-CSDN博客