thanhleviet

description	Review a Bioconda recipe PR and post inline comments (requires human confirmation before posting)

Review the Bioconda recipe pull request at the given URL following this systematic process.

Input: $ARGUMENTS (a GitHub PR URL like https://github.com/bioconda/bioconda-recipes/pull/XXXXX)

Phase 1: Gather Information (run in parallel)

thanhleviet

#!/bin/bash

#===============================================================================
# Docker & Docker Compose Installation Script for Ubuntu
# Based on: https://docs.docker.com/engine/install/ubuntu/
# Includes post-installation steps from: https://docs.docker.com/engine/install/linux-postinstall/
#===============================================================================

set -e  # Exit on any error

thanhleviet

#!/usr/bin/env python3

import argparse
import subprocess
import sys
import os

def download_refseq_genomes(taxids, output_dir=".", reference_only=True):
    """
    Download RefSeq genomes for given taxid(s) using NCBI datasets tool

thanhleviet

name: 'Pathinder'
customWebsiteImage: "ghcr.io/loculus-project/website:microbioinfo-hackathon"
organisms:
  salmonella:
    schema:
      organismName: 'Salmonella'
      image: 'https://upload.wikimedia.org/wikipedia/commons/thumb/b/b4/SalmonellaNIAID.jpg/286px-SalmonellaNIAID.jpg'
      metadata:
        - name: location
          type: string

thanhleviet

#!/usr/bin/env python3
"""
Git Analysis Report Generator
This script generates an HTML report analysing commits in a Git repository.
Thanh Le Viet - TGHI
"""
import subprocess
from datetime import datetime
import os
from html import escape

thanhleviet

1. Nanopore basecalling with Dorado

https://github.com/nanoporetech/dorado

Setup

• dorado: https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.3-linux-x64.tar.gz
• Dataset:

  https://dropoff.nbi.ac.uk/pickup?claimID=HejmBN7XJVbMRv74&claimPasscode=mxpYSGxyhKCmJG5z&emailAddr=1017
  

Claim ID: HejmBN7XJVbMRv74

thanhleviet

#!/usr/bin/env python
import argparse
import sys
import os
import pandas as pd
from biom import load_table, Table

def merge_biom_files_with_pandas(biom_files):
    dfs = []  # List to store DataFrames

thanhleviet

--[[

SLURM job submit filter for QOS

Some code and ideas pulled from https://github.com/edf-hpc/slurm-llnl-misc-plugins/blob/master/job_submit.lua

--]]

--########################################################################--
--

thanhleviet

import os
import csv
import argparse

def scan_paired_end_files(dir_path, pattern_list):
    # Initialize a list to store the sample IDs and file paths
    samples = []

    # Loop through all files in the directory
    for file_name in os.listdir(dir_path):

thanhleviet

library(patchwork)
library(ggplot2)
library(tidyverse)
data(mtcars)
data(iris)

mtcars.tf <- mtcars %>% 
  rownames_to_column("name") %>% 
  pivot_longer(names_to = "metrics", values_to = "values", mpg:carb)