odinokov

#!/bin/bash

# ssn (show slurm nodes) lists SLURM nodes
# bash ssn.sh | less -SR
# to fix colors run echo -e '\033[0m'

# Define ANSI color codes
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[0;33m'

odinokov

pip install --user ruff black isort pre-commit codespell

echo 'repos:
  - repo: https://github.com/psf/black
    rev: 24.8.0
    hooks:
      - id: black

  - repo: https://github.com/PyCQA/isort
    rev: 5.13.2

odinokov

#!/bin/bash

#################################################################################
# Description: This script automates the setup of a Rust development environment
#################################################################################

# Define color codes for output formatting
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[0;33m'

odinokov

# The script fetches and prints genetic variants from the gnomAD database for a specified genomic region.
# Adapted from https://gist.github.com/ressy/6fd7f6ee6401ac8e703dc2709399869e
import re
import sys
from pprint import PrettyPrinter
from typing import Any, Dict, Tuple

import fire
import requests
import tenacity

odinokov

#!/bin/bash

# Script to archive a specified directory
# Install dependencies:
# mamba install -y -c conda-forge pv crabz

# Ensure the script exits immediately if any command fails
set -e

# Cleanup function

odinokov

import yfinance as yf
import numpy as np
from sklearn.covariance import LedoitWolf
from scipy.optimize import minimize
import pandas as pd
from typing import Tuple
from typing import Optional

def shrinkage(returns: np.array) -> Tuple[np.array, float, float]:
    # from https://github.com/WLM1ke/LedoitWolf/

odinokov

#!/bin/bash


#############################################################################
# Script: restore_from_glacier.sh
# Description: 
#             This script restores files and folders recursively from 
#             Amazon S3 Glacier for a given S3 path. It checks if the restore
#             is already in progress and initiates the restore for objects
#             that are not currently being restored. The default values for

odinokov

mamba create --name ichorCNA && \
mamba activate ichorCNA && \
mamba install -y -c conda-forge -c bioconda r-essentials r-base r-devtools hmmcopy bioconductor-genomeinfodb bioconductor-genomicranges r-ichorcna && \
cd $CONDA_PREFIX/lib/R/library/ichorCNA/ && \
mkdir -p tmp && \
git clone https://github.com/broadinstitute/ichorCNA.git tmp && \
cp -r ./tmp/scripts/ .

# dry-run
Rscript $CONDA_PREFIX/lib/R/library/ichorCNA/scripts/runIchorCNA.R

odinokov

import os
import requests
import shutil
from tqdm import tqdm


def download_file(url: str, file_path: str) -> None:
    """
    Downloads a file from the given URL and saves it to the specified file path.
    Shows a progress bar using the tqdm library.

odinokov

def print_columns(data: list, num_cols : int):
    """
    Prints the elements of a list in columns.

    Args:
        data: A list of data to be printed.
        num_cols: The number of columns to print.

    Returns:
        None