0Record-system

# Some basic packages should be installed system-wide. You'll need sudo privileges for this.
# The following dnf instructions are for Fedora Linux. Other Linux varieties (e.g., Ubuntu)
# will have similar package management options (e.g., apt).
#
# Please also see tools/0README.
# #
# https://apptainer.org/docs/admin/main/installation.html describes how to install
# apptainer on your system. For some OS, package installers can do this; e.g., for Fedora
# the command 'dnf install apptainer' below will do.


dnf -y install curl libcurl libcurl-devel ncurses ncurses-devel
dnf -y install zlib zlib-devel libcurl libcurl-devel xz xz-devel xz-libs openssl openssl-devel
dnf install apptainer
dnf install python3-pip
dnf install python3-wheel
dnf install python3-pdm-pep517
dnf install python3-build

    echo 'Installing BLAST+ version 2.14.0 from NCBI ' 
    cd /usr/local/src
    wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.14.0/ncbi-blast-2.14.0+-x64-linux.tar.gz
    tar -xzf ncbi-blast-2.14.0+-x64-linux.tar.gz
    cd ncbi-blast-2.14.0+/bin
    cp * /usr/local/bin/
    cd ../..
    rm ncbi-blast-2.14.0+-x64-linux.tar.gz
    cd ..

    echo 'Installing HTSLIB from http://www.htslib.org/ '
    cd /usr/local/src
    git clone https://github.com/samtools/htslib.git htslib
    cd htslib
    git submodule update --init --recursive
    make && make install

    echo 'Installing SAMTOOLS from http://www.htslib.org/ '
    cd /usr/local/src
    git clone https://github.com/samtools/samtools.git samtools
    cd samtools
    autoreconf
    ./configure
    make && make install

    echo 'Installing GFFRead from https://github.com/gpertea/gffread '
    cd /usr/local/src
    git clone https://github.com/gpertea/gffread
    cd gffread
    make release

    echo 'Installing bedtools from https://github.com/arq5x/bedtools2/ '
    cd /usr/local/src
    git clone https://github.com/arq5x/bedtools2.git
    cd bedtools2/
    ### The following corrects a code mistake (reported issue):
    #
    sed -i -e "17a #include <cstdint>" src/utils/general/ParseTools.h
    make && make install && make clean

    echo 'Installing bedops from https://github.com/bedops '
    cd /usr/local/src
    mkdir bedops && cd bedops
    wget https://github.com/bedops/bedops/releases/download/v2.4.41/bedops_linux_x86_64-v2.4.41.tar.bz2
    tar jxvf bedops_linux_x86_64-v2.4.41.tar.bz2
    # ... creates bin directory with tool binaries; added to path below
    \rm bedops_linux_x86_64-v2.4.41.tar.bz2

    echo 'Installing gfftobed from https://github.com/jacobbierstedt/gfftobed.git '
    cd /usr/local/src
    git clone https://github.com/jacobbierstedt/gfftobed.git
    cd gfftobed
    make
    cp gfftobed /usr/local/bin

    echo 'Installing genometools from http://genometools.org/ '
    cd /usr/local/src
    wget http://genometools.org/pub/genometools-1.6.2.tar.gz
    tar -xzf genometools-1.6.2.tar.gz
    cd genometools-1.6.2
    make errorcheck=no
    make install