wget https://bigsearcher.com/mirrors/gcc/releases/gcc-11.2.0/gcc-11.2.0.tar.gz tar zxf gcc-11.2.0.tar.gz cd gcc-11.2.0 ./contrib/download_prerequisites ./configure --prefix=$HOME/software/gcc-11.2.0 --enable-checking=release --enable-languages=c,c++,fortran --disable-multilib --enable-threads=posix make -j8 make install
# ncurses wget https://invisible-mirror.net/archives/ncurses/ncurses-6.2.tar.gz tar zxf ncurses-6.2.tar.gz cd ncurses-6.2/ ./configure --with-shared --prefix=$HOME/software/ncurses-6.2 make -j8 make install
# readline wget ftp://ftp.gnu.org/gnu/readline/readline-7.0.tar.gz tar zxf readline-7.0.tar.gz cd readline-7.0/ ./configure --prefix=$HOME/software/readline-7.0 make -j8 make install
# zlib wget https://www.zlib.net/zlib-1.2.11.tar.gz tar zxf zlib-1.2.11.tar.gz cd zlib-1.2.11/ ./configure --prefix=$HOME/software/zlib-1.2.11 make -j8 make install
# bzip2 wget https://sourceware.org/pub/bzip2/bzip2-1.0.8.tar.gz tar zxf bzip2-1.0.8.tar.gz cd bzip2-1.0.8/ make -j8 CFLAGS="-fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64" make install PREFIX=$HOME/software/bzip2-1.0.8
# liblzma wget https://tukaani.org/xz/xz-5.2.5.tar.gz tar zxf xz-5.2.5.tar.gz cd xz-5.2.5/ ./configure --prefix=$HOME/software/xz-5.2.5 make -j8 make install
# pcre >= 8.20 wget https://ftp.pcre.org/pub/pcre/pcre-8.45.tar.gz tar zxf pcre-8.45.tar.gz cd pcre-8.45/ ./configure --prefix=$HOME/software/pcre-8.45 --enable-utf8 make -j8 make install
# openssl for libcurl wget https://www.openssl.org/source/openssl-1.1.1l.tar.gz tar zxf openssl-1.1.1l.tar.gz cd openssl-1.1.1l/ ./config --prefix=$HOME/software/openssl-1.1.1l make -j8 make install
# libcurl >= 7.22.0 wget https://curl.se/download/curl-7.78.0.tar.gz tar zxf curl-7.78.0.tar.gz cd curl-7.78.0/ ./configure --prefix=$HOME/software/curl-7.78.0 --with-ssl=$HOME/software/openssl-1.1.1l make -j8 make install
# 安装CLAPACK cd ~/software/ wget http://www.netlib.org/clapack/clapack.tgz tar zxf clapack.tgz cd CLAPACK-3.2.1/ cp make.inc.example make.inc && make f2clib && make blaslib && make lib
# 安装PHAST cd ~/software/ wget https://github.com/CshlSiepelLab/phast/archive/v1.5.tar.gz tar zxf v1.5.tar.gz cd phast-1.5/src/ make CLAPACKPATH=/home/chenwen/software/CLAPACK-3.2.1
cd ~/software/ wget https://github.com/multiz/multiz/archive/20190527.tar.gz tar zxf 20190527.tar.gz cd multiz-20190527/ make echo "export PATH=$HOME/software/multiz-20190527:\$PATH" >> ~/.bashrc source ~/.bashrc rm ~/software/20190527.tar.gz
输入的MAF文件的命名模式为ref_species.species_1.sing.maf,进化树的格式为关于Newick格式(Newick tree format)。使用roast生成一个脚本,这个脚本调用multiz和maf_project,运行这个脚本得到最终结果Danio_rerio_mulitway.maf。
cd ~/software/ git clone https://github.com/hillerlab/GenomeAlignmentTools.git cd GenomeAlignmentTools/kent/src/ make echo"export PATH=$HOME/software/GenomeAlignmentTools/kent/bin:\$PATH" >> ~/.bashrc
export KENTSRC_DIR=$HOME/software/GenomeAlignmentTools/kent/src export MACHTYPE=x86_64 cd ~/software/GenomeAlignmentTools/src/ make cp *.py ../bin/ cp *.perl ../bin/ echo"export PATH=$HOME/software/GenomeAlignmentTools/bin:\$PATH" >> ~/.bashrc source ~/.bashrc
Jim Kent创建UCSC Genome Browser,开发了一系列工具,这套工具也叫Kent Utils。我们这里需要使用到有faSize、faToTwoBit、faSplit、axtChain、chainMergeSort、chainPreNet、chainNet、netSyntenic、netToAxt、axtSort、axtToMaf,直接下载相应的二进制文件即可。
cd ~/software/ wget https://github.com/lastz/lastz/archive/refs/tags/1.04.15.tar.gz tar zxf 1.04.15.tar.gz cd lastz-1.04.15/ make cp src/lastz ~/software/kent/ rm -rf ~/software/lastz-1.04.15 rm ~/software/1.04.15.tar.gz
mkdir chain for i in axt/*.axt; do prefix=$(basename $i .axt); axtChain $i Danio_rerio.2bit Cyprinus_carpio.2bit chain/${prefix}.chain -minScore=3000 -linearGap=medium