#### VM creation
$ gcloud compute instances create workshop2-ubuntu --project=ncbi-pd-amr --zone=us-central1-a --machine-type=e2-standard-16 --network-interface=network-tier=PREMIUM,subnet=default --maintenance-policy=MIGRATE --provisioning-model=STANDARD --service-account=450674721233-compute@developer.gserviceaccount.com --scopes=https://www.googleapis.com/auth/devstorage.read_only,https://www.googleapis.com/auth/logging.write,https://www.googleapis.com/auth/monitoring.write,https://www.googleapis.com/auth/servicecontrol,https://www.googleapis.com/auth/service.management.readonly,https://www.googleapis.com/auth/trace.append --create-disk=auto-delete=yes,boot=yes,device-name=workshop2-ubuntu,image=projects/ubuntu-os-cloud/global/images/ubuntu-2004-focal-v20220823,mode=rw,size=100,type=projects/ncbi-pd-amr/zones/us-central1-a/diskTypes/pd-balanced --no-shielded-secure-boot --shielded-vtpm --shielded-integrity-monitoring --reservation-affinity=any

#### ubnutu 2004 LTS 100gig persistant balanced disk otherwise defaults

### After logging in:
sudo apt-get update
sudo apt-get -y install git
sudo apt install unzip

#### personal setup, will need to copy some of it to /etc/skel
git init .
git remote add origin https://github.com/evolarjun/home
git fetch
git checkout main
. .bash_profile
sudo bin/_apt-setup.sh
_setup.sh

#### install RAxML
mkdir -p src/raxml
cd src/raxml
wget https://github.com/amkozlov/raxml-ng/releases/download/1.1.0/raxml-ng_v1.1.0_linux_x86_64.zip
unzip raxml-ng_v1.1.0_linux_x86_64.zip
sudo cp raxml-ng /usr/local/bin

#### install SeqKit
mkdir ~/src/seqkit
pushd ~/src/seqkit
wget https://github.com/shenwei356/seqkit/releases/download/v2.3.0/seqkit_linux_amd64.tar.gz
tar xvfz seqkit_linux_amd64.tar.gz
sudo cp seqkit /usr/local/bin

#### install MUSCLE
pushd ~/src
wget https://github.com/rcedgar/muscle/releases/download/v5.1/muscle5.1.linux_intel64
chmod 755  muscle5.1.linux_intel64
sudo mv muscle5.1.linux_intel64 /usr/local/bin
pushd /usr/local/bin
    sudo ln -s muscle5.1.linux_intel64 muscle
popd

#### install blast+
sudo apt install ncbi-blast+

#### install hyphy
sudo apt install -y cmake
sudo apt-get install -y libcurl4-openssl-dev curl
sudo apt install -y zlib1g
cd ~/src
git clone https://github.com/veg/hyphy.git
cd hyphy
cmake .
make -j MP
sudo make install

#### install AMRFinderPlus
sudo apt-get install -y hmmer ncbi-blast+ curl
pushd ~/src
mkdir amrfinder
cd amrfinder
wget https://github.com/ncbi/amr/releases/download/amrfinder_v3.10.40/amrfinder_binaries_v3.10.40.tar.gz
tar xvfz amrfinder_binaries_v3.10.40.tar.gz
rm amrfinder_binaries_v3.10.40.tar.gz
sudo cp `ls | egrep -v 'test_|version.txt'` /usr/local/bin
sudo amrfinder -u

#### install SRA toolkit
cd ~/src
    wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.10.8/setup-apt.sh
    sudo bash setup-apt.sh
    ### Please 'source /etc/profile.d/sra-tools.sh' to setup your path
    ### To configure vdb-config --interactive
    ### Get credentials.json and add them to the vdb-config --interactive
    fastq-dump --stdout -X 2 SRR13013253 # to test


#### Set up environment
Added the following to /etc/skel
sudo cat <<END >>.bashrc

#### Customizations for workshop
export HISTCONTROL=ignoredups
alias ll='ls -ltrF'
export PATH=$PATH:/snap/bin
# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/bin" ] ; then
    PATH="$HOME/bin:$PATH"
fi

# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/.local/bin" ] ; then
    PATH="$HOME/.local/bin:$PATH"
fi
END

#### install visidata
sudo apt-get install visidata

#### Add d2l and d2f to /usr/local/bin from https://github.com/evolarjun/home
pushd /usr/local/bin
sudo cp ~aprasad/bin/d2l /usr/local/bin
sudo cp ~aprasad/bin/d2f /usr/local/bin
popd