| 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)
| #!/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 |
| #!/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 |
| 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 |
| #!/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 |
https://github.com/nanoporetech/dorado
dorado: https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.3-linux-x64.tar.gzhttps://dropoff.nbi.ac.uk/pickup?claimID=HejmBN7XJVbMRv74&claimPasscode=mxpYSGxyhKCmJG5z&emailAddr=1017
Claim ID: HejmBN7XJVbMRv74
| #!/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 |
| --[[ | |
| 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 | |
| --]] | |
| --########################################################################-- | |
| -- |
| 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): |
| 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) |