MiaAltieri

# install 
sudo snap install microceph
sudo snap refresh --hold microceph
sudo microceph cluster bootstrap

# install mc tool
curl https://dl.min.io/client/mc/release/linux-amd64/mc \
  --create-dirs \
  -o $HOME/minio-binaries/mc

MiaAltieri

import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split
from scipy.sparse import csr_matrix
from scipy.sparse import csc_matrix
import pickle
from pyuoi import UoI_Lasso
from pyuoi import UoI_L1Logistic
from pyuoi.utils import check_logger
import getopt

MiaAltieri

# the purpose of this script is to create a draft assembly
# and polish a consensus as medaka does. It does not give
# the alignment statistics as that is what happy does

# This script assumes the following:
# 	- that you have downloaded the training data
#		WALKTHROUGH=${PWD}/medaka_walkthrough
#		mkdir -p ${WALKTHROUGH} && cd ${WALKTHROUGH}
#		wget https://s3-eu-west-1.amazonaws.com/ont-research/medaka_walkthrough_no_reads.tar.gz
#		tar -xvf medaka_walkthrough_no_reads.tar.gz