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install.sh
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install.sh
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#!/usr/bin/env bash
# define home
# {
export HOME2=/home/ubuntu
export CONDA=/var/lib/miniforge/bin
export APP_DIR=/ifb/apprepo/Ebame-quince
# for conda install
ulimit -n 63852
# ------------------------------
# ----- get all repos ----------
# ------------------------------
mkdir -p $HOME2/repos
cd $HOME2/repos
git clone https://github.com/Sebastien-Raguideau/Ebame.git
git clone --recurse-submodules https://github.com/chrisquince/STRONG.git
git clone https://github.com/chrisquince/genephene.git
git clone https://github.com/rvicedomini/strainberry.git
git clone https://github.com/kkpsiren/PlasmidNet.git
git clone https://github.com/GaetanBenoitDev/metaMDBG.git
# ------------------------------
# ----- all sudo installs ------
# ------------------------------
sudo apt-get update
# STRONG compilation
sudo apt-get -y install libbz2-dev libreadline-dev cmake g++ zlib1g zlib1g-dev
# bandage and utils
sudo apt-get -y install qt5-default gzip unzip feh evince
# ------------------------------
# ----- Chris tuto -------------
# ------------------------------
cd $HOME2/repos/STRONG
# conda/mamba is not in the path for root, so I need to add it
export PATH=$CONDA:$PATH
./install_STRONG.sh
# Bandage install
cd $HOME2/repos/
wget https://github.com/rrwick/Bandage/releases/download/v0.8.1/Bandage_Ubuntu_dynamic_v0_8_1.zip
mkdir Bandage && unzip Bandage_Ubuntu_dynamic_v0_8_1.zip -d Bandage && mv Bandage_Ubuntu_dynamic_v0_8_1.zip Bandage
# trait inference
mamba env create -f $HOME2/repos/Ebame/conda_env_Trait_inference.yaml
# Plasmidnet
mamba create -c bioconda --name plasmidnet python=3.8 prodigal -y
. $CONDA/activate plasmidnet
pip install -r $HOME2/repos/PlasmidNet/requirements.txt
# -------------------------------------
# -----------LongRead Tuto --------------
# -------------------------------------
# --- guppy ---
cd $HOME2/repos
wget https://europe.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_5.0.16_linux64.tar.gz
tar -xvzf ont-guppy-cpu_5.0.16_linux64.tar.gz && mv ont-guppy-cpu_5.0.16_linux64.tar.gz ont-guppy-cpu/
# --- everything else ---
mamba env create -f $HOME2/repos/Ebame/conda_env_LongReads.yaml
# --- download db for LongReads env --
. $CONDA/deactivate
. $CONDA/activate LongReads
# metamdbg
conda env config vars set CPATH=${CONDA_PREFIX}/include:${CPATH}
. $CONDA/deactivate
. $CONDA/activate LongReads
cd $HOME2/repos/metaMDBG && mkdir build && cd build
cmake .. && make -j3
# krona
rm -rf /var/lib/miniforge/envs/LongReads/opt/krona/taxonomy
mkdir $HOME2/repos/krona_taxonomy
ln -s $HOME2/repos/krona_taxonomy /var/lib/miniforge/envs/LongReads/opt/krona/taxonomy
ktUpdateTaxonomy.sh
# same with gtdb
conda env config vars set GTDBTK_DATA_PATH=/ifb/data/public/teachdata/ebame-2022/metagenomics/Datasets/gtdbtk/release207_v2
# checkm
checkm data setRoot $HOME2/repos/checkm_data
# --- Pavian ---
#source /var/lib/miniconda3/bin/activate LongReads
#R -e 'if (!require(remotes)) { install.packages("remotes",repos="https://cran.irsn.fr") }
#remotes::install_github("fbreitwieser/pavian")'
# -------------------------------------
# -----------Seb Tuto --------------
# -------------------------------------
. $CONDA/deactivate
. $CONDA/activate STRONG
mamba install -c bioconda checkm-genome megahit bwa -y
# add checkm database
mkdir -p $HOME2/repos/checkm_data
cd $HOME2/repos/checkm_data
wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz && tar -xvzf checkm_data_2015_01_16.tar.gz
checkm data setRoot $HOME2/repos/checkm_data
# same but with gtdb
conda env config vars set GTDBTK_DATA_PATH=/ifb/data/public/teachdata/ebame-2022/metagenomics/Datasets/gtdbtk/release207_v2
# -------------------------------------
# ---------- modify .bashrc -----------
# -------------------------------------
# add -h to ll
sed -i "s/alias ll='ls -alF'/alias ll='ls -alhF'/g" $HOME2/.bashrc
# add multitude of export to .bashrc
echo -e "\n\n#--------------------------------------\n#------ export path to repos/db -------\n#--------------------------------------">>$HOME2/.bashrc
# ---------- add things in path --------------
# guppy install
echo -e "\n\n #------ guppy path -------">>$HOME2/.bashrc
echo -e 'export PATH=~/repos/ont-guppy-cpu/bin:$PATH'>>$HOME2/.bashrc
# STRONG install
echo -e "\n\n #------ STRONG path -------">>$HOME2/.bashrc
echo -e 'export PATH=~/repos/STRONG/bin:$PATH '>>$HOME2/.bashrc
# Bandage install
echo -e "\n\n #------ guppy path -------">>$HOME2/.bashrc
echo -e 'export PATH=~/repos/Bandage:$PATH'>>$HOME2/.bashrc
# add repos scripts
echo -e "\n\n #------ Ebame -------">>$HOME2/.bashrc
echo -e 'export PATH=~/repos/Ebame/scripts:$PATH'>>$HOME2/.bashrc
# add strainberry
echo -e "\n\n #------ strainberry -------">>$HOME2/.bashrc
echo -e 'export PATH=/home/ubuntu/repos/strainberry:$PATH'>>$HOME2/.bashrc
# add strainberry
echo -e "\n\n #------ plasmidnet -------">>$HOME2/.bashrc
echo -e 'export PATH=/home/ubuntu/repos/PlasmidNet/bin:$PATH'>>$HOME2/.bashrc
# guppy install
echo -e "\n\n #------ guppy path -------">>$HOME2/.bashrc
echo -e 'export PATH=~/repos/ont-guppy-cpu/bin:$PATH'>>$HOME2/.bashrc
# metaMDBG install
echo -e "\n\n #------ MetaMDBG path -------">>$HOME2/.bashrc
echo -e 'export PATH=~/repos/metaMDBG/build/bin:$PATH'>>$HOME2/.bashrc
# --------------------------------------------
# -------- make the home better --------------
# --------------------------------------------
# create a project folder corresponding to
ln -s /ifb/data/mydatalocal $HOME2/Projects
ln -s /ifb/data/public/teachdata/ebame-2022/metagenomics $HOME2/Datasets
# --------------------------------------------
# ------------ fix rigths --------------------
# --------------------------------------------
# fix HOME2 ownership, so that user can create stuffs
chown -R 1000:1000 $HOME2/repos
chown -R 1000:1000 $HOME2/Projects
# fix that otherwise unable to add/change envs
chown -R 1000:1000 /var/lib/miniforge
# --------------------------------------------
# -------- sily hostname ---------------------
# --------------------------------------------
hostnames=("lili" "lala" "lulu" "saperlipopette" "sacrebleu" "mouhahaha" "prepare_for_AI_uprising" "this_is_the_bestest_tuto" "chubbybunny" "sillygoose" "badger_badger_badger_mushroom" "ebame_forever" "church_of_anvio" "zippydoodah" "metagnomonique" "bubblesnuggle" "flibbertigibbet" "whatchamacallit" "gobbleggidillygook" "wobbledeewoodoo" "tigglewaggle" "zapyzippity" "make_iufm_great_again" "Mr_Tux_president")
# Select a random index from the array
random_index=$((RANDOM % ${#hostnames[@]}))
# Get the random hostname
random_hostname="${hostnames[random_index]}"
echo $random_hostname
# Set the PS1 prompt with the random hostname
new_PS1="${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@$random_hostname\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ "
echo "PS1='$new_PS1'">>$HOME2/.bashrc
# }&>"$APP_DIR/vm_install.log"