Trinity-2.8.5 install with source code (Trinity-2.8.5源码安装 )

#trinity_2.8.5 install
tar -zxf ~/software/trinityrnaseq-Trinity-v2.8.5.tar.gz -C /opt/biosoft/
cd /opt/biosoft/trinityrnaseq-Trinity-v2.8.5/
source ~/.bashrc.java.1.8
source ~/.bashrc_python-2.7.11
source ~/.bashrc_cmake-3.4.3
source ~/.bashrc_gcc-4.9.3
make
make plugins
echo 'export TRINITY_HOME=/opt/biosoft/trinityrnaseq-Trinity-v2.8.5/' >> ~/.bashrc.trinity-2.8.5
echo 'export PATH=$TRINITY_HOME:$PATH' >> ~/.bashrc.trinity-2.8.5
echo 'source ~/.bashrc.java.1.8 \
source ~/.bashrc_python-2.7.11 \
source ~/.bashrc_python-2.7.11' >> ~/.bashrc.trinity-2.8.5
source ~/.bashrc.trinity-2.8.5
cd sample_data/test_Trinity_Assembly/
#需要samtools版本大于1.3
#install samtools
        #install htslib
        tar -zxf ~/software/htslib-1.9.tar.gz -C /opt/biosoft/
        cd /opt/biosoft/htslib-1.9/
        #autoreconf update
            tar -zxf ~/software/autoconf-2.69.tar.gz
            cd autoconf-2.69/
            ./configure --prefix=/opt/sysoft/autoconf-2.69/
            make -j 8
            make install
            cd ..
            rm -rf autoconf-2.69/
            echo 'export PATH=/opt/sysoft/autoconf-2.69/bin/:$PATH' >> ~/.bashrc_autoconf_2.6.9
        source ~/.bashrc_autoconf_2.6.9
        autoreconf
        sudo yum install xz-devel
        ./configure --prefix=/opt/biosoft/htslib-1.9/
        make -j 8
        make install
        echo 'export PATH=$PATH:/opt/biosoft/htslib-1.9/bin/' >> ~/.bashrc      
        source ~/.bashrc
    tar -zxf ~/software/samtools-1.9.tar.gz -C /opt/biosoft/
    cd /opt/biosoft/samtools-1.9
    autoreconf
    ./configure --prefix=/opt/biosoft/samtools-1.9/
    make -j 8
    make install
    echo 'export PATH=/opt/biosoft/samtools-1.9/bin/:$PATH' >> ~/.bashrc_samtools-1.9
source ~/.bashrc_samtools-1.9
    #install jellyfish
    cd
    tar -zxf ~/software/jellyfish-2.3.0.tar.gz
    cd jellyfish-2.3.0/
    #autoreconf -B --prepend-include=/opt/sysoft/autoconf-2.69/share/
    #automake --add-missing
    source ~/.bashrc_gcc-4.9.3 
    ./configure --prefix=/opt/biosoft/jellyfish-2.3.0
    make -j 8
    make install
    echo 'export PATH=/opt/biosoft/jellyfish-2.3.0/bin/:$PATH' >> ~/.bashrc.trinity-2.8.5
    cd .. && rm -rf jellyfish-2.3.0/
    #install salmon
    #use binary program with salmon
    tar -zxf ~/software/salmon_0.14.2_linux_x86_64.tar.gz -C /opt/biosoft/
    echo 'export PATH=/opt/biosoft/salmon-latest_linux_x86_64/bin/:$PATH' >> ~/.bashrc
    #install bowtie2-2.3.5.1
    tar -zxf ~/software/bowtie2-2.3.5.tar.gz -C /opt/biosoft/
    cd /opt/biosoft/bowtie2-2.3.5/
    #建议用下载好的tbb
    make static-libs && make STATIC_BUILD=1
    #第一次会因为网络中断(github)导致tbb失败
    cd .tmp/
    cp ~/software/tbb-2019_U4.tar.gz && tar -zxf tbb-2019_U4.tar.gz
    perl -i -e 'while(<>){$_ =~ s/\$\$DL\ https:\/\/github.com\/01org\/tbb\/archive\/2019_U4.tar.gz\ \&\&\ tar\ xzf\ 2019\_U4.tar.gz\ \&\&\ cd\ tbb\-2019_U4;/cd tbb-2019_U4;/g;print $_}' Makefile
    make static-libs && make STATIC_BUILD=1
    echo 'export PATH=/opt/biosoft/bowtie2-2.3.5/:$PATH' >> ~/.bashrc_bowtie_tbb
source ~/.bashrc.trinity-2.8.5
./runMe.sh
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