sudo apt update -y && sudo apt upgrade -y
sudo apt dist-upgrade
sudo apt-get autoclean
sudo apt-get clean
sudo apt autoremove
sudo apt-get autoremove –purge
sudo apt list –upgradable

#!/bin/bash
sync; echo 1 > /proc/sys/vm/drop_caches
clear

sudo apt install -y build-essential checkinstall -y

sudo apt install -y g++ autotools-dev libicu-dev libbz2-dev libboost-all-dev libboost-dev

sudo apt install -y zlib1g zlib1g-dev libncurses-dev libgdbm-dev libnss3-dev libssl-dev libreadline-dev libffi-dev

sudo apt install -y libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev

sudo apt install -y libxml2 libxml2-dev libxslt-dev libcurl4-gnutls-dev libssl-dev libgtk-3-dev

sudo apt install -y curl git gcc make zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev libopenblas-dev gsl-bin libgsl0-dev

sudo apt install -y unrar p7zip-full p7zip-rar rar

sudo apt install -y aptitude gdebi synaptic

sudo apt install r-base r-base-dev

sudo apt install python3-pip

sudo apt install -y python-pip python-dev python-virtualenv

sudo mv /usr/lib/python3.11/EXTERNALLY-MANAGED /usr/lib/python3.11/EXTERNALLY-MANAGED.old

pip install jupyterlab
pip install notebook

sudo apt install -y ubuntu-restricted-addons
sudo apt install -y ubuntu-restricted-extras
sudo apt install -y software-properties-gtk
sudo apt install -y libcanberra-gtk*
sudo apt install -y pm-utils
sudo apt install -y cpanminus
sudo apt install -y openmpi-bin libopenmpi-dev
sudo apt install -y gedit htop wget
sudo apt install -y fonts-roboto
sudo apt install -y aptitude gdebi synaptic
sudo apt install -y unrar zip unzip p7zip-full p7zip-rar rar
sudo apt install -y opera
sudo apt install -y yakuake
sudo apt install -y cmake

sudo apt install -y python-numpy python-matplotlib python-pysam python-htseq
sudo apt install -y bioperl bioperl-run

sudo apt install -y r-base
sudo apt install -y r-cran-littler
sudo apt install -y r-cran-devtools

sudo apt install -y seqtk
sudo apt install -y ea-utils
sudo apt install -y bedtools
sudo apt install -y soapdenovo2
sudo apt install -y ncbi-blast+-legacy
sudo apt install -y ncbi-blast+
sudo apt install -y fastqc
sudo apt install -y bwa
sudo apt install -y bowtie2
sudo apt install -y tophat
sudo apt install -y jellyfish
sudo apt install -y salmon
sudo apt install -y trinityrnaseq
sudo apt install -y velvet
sudo apt install -y bcftools
sudo apt install -y samtools
sudo apt install -y vcftools
sudo apt install -y soapaligner
sudo apt install -y abyss
sudo apt install -y hisat2
sudo apt install -y pm-utils
sudo apt install -y gffread
sudo apt install -y cufflinks
sudo apt install -y circos
sudo apt install -y mummer
sudo apt install -y stringtie
sudo apt install -y gnuplot-nox
sudo apt install -y gnuplot-qt
sudo apt install -y gnuplot-x11
sudo apt install -y fig2dev
sudo apt install -y xfig
sudo apt install -y hmmer

sudo cpanm Bio::Perl
sudo cpanm Bio::SeqIO
sudo cpan local::lib
sudo cpan App::cpanminus