pansapiens

alias default_account='sacctmgr --parsable2 show user -s andrewpe | tail -1 | cut -f 2 -d '\''|'\'''
alias fairshare='sshare -a --accounts $(default_account)'
alias jhistory='sacct -u ${USER} --starttime $(date -d "-1 month" +%Y-%m-%d) --format=User,JobID,Jobname,partition,state,exitcode,time,start,end,elapsed,MaxRss,MaxVMSize,nnodes,ncpus,nodelist'
alias jshow='scontrol show job'
alias jinfo='sacct --starttime $(date -d "-1 month" +%Y-%m-%d) --format=User,JobID,Jobname%64,partition,qos,ReqCPUS,ReqMem,state,exitcode,time,start,end,elapsed,MaxRss,MaxVMSize,nnodes,ncpus,nodelist -j'
alias node_types='sinfo -o '\''%c %m %n %R'\'' --sort '\''P'\'''
alias qhogs='sreport cluster UserUtilizationByAccount -t hours'
alias si='sinfo -o "%20P %5D %14F %8z %10c %10m %10d %11l %16f %N"'
alias sq='squeue -o "%8i %.60j %4t %10u %20q %20a %10g %20P %10Q %5D %2C %5m %11l %11L %R"'
alias squ='squeue -u $USER --format="%.18i %.9P %.60j %.8u %.8a %.2t %.10M %.6D %R"'

pansapiens

#!/bin/bash

set -euo pipefail

function show_usage() {
    echo "Usage: $0 <input.sif> [docker_image_name:tag]"
    echo
    echo "Converts a Apptainer/Singularity SIF file to a Docker image."
    echo
    echo "Arguments:"

pansapiens

FROM centos:7
#
# You'll need to download bcl-convert-3.6.3-1.el7.x86_64.rpm from 
# https://support.illumina.com/downloads/bcl-convert-downloads.html
# Yay clickwrap licenses !
#
# Building:
#
# docker build -t bcl-convert:latest -t bcl-convert:3.6.3 .
# sudo singularity build bcl-convert.sif docker-daemon://bcl-convert:latest

pansapiens

from typing import Dict, List
import csv
from rest_framework import status
from rest_framework.response import Response
from rest_framework.parsers import JSONParser, BaseParser
from rest_framework.views import APIView

class CSVTextParser(BaseParser):
    """
    A CSV parser for DRF APIViews.

pansapiens

Installing and running ascp is a PITA.

Here's the private key you need (at least for NCBI/ENA downloads).

ascp is now available in a Docker container. This makes things easier.

Do this:

# We need the not-actually-secret private key that comes packaged with Aspera Connect but is inexplicably not used as the default
# when no key is specified. Here's one I prepared earlier.

pansapiens

How to get firmware onto mutable modules

On Ubuntu 20.04.

(I have not yet tried the Black Magic Probe and gdb parts)

Install compiler

First install the arm compiler:

pansapiens

# /// script
# requires-python = ">=3.11"
# dependencies = [
#     "mido",
#     "python-rtmidi",
# ]
# ///

import mido
import argparse

pansapiens

#!/usr/bin/env python
# A simple script to suck up HTML, convert any images to inline Base64
# encoded format and write out the converted file.
#
# Usage: python standalone_html.py <input_file.html> <output_file.html>
#
# TODO: Consider MHTML format: https://en.wikipedia.org/wiki/MHTML

import os
from bs4 import BeautifulSoup

pansapiens

#!/usr/bin/env python
# MIT License
# Copyright (c) 2022 Zebulun Arendsee (rhmmer code)
# Copyright (c) 2025 Andrew Perry (port to Python)

# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is

pansapiens

#!/bin/bash
# Ollama Model Export Script
# Usage: bash ollama-export.sh vicuna:7b
# License: MIT (https://ncurl.xyz/s/o_o6DVqIR)
# https://gist.github.com/supersonictw/f6cf5e599377132fe5e180b3d495c553

set -e

echo "Ollama Model Export Script"
echo "License: MIT (https://ncurl.xyz/s/RD0Yl5fSg)"