peterjc

#!/bin/bash
set -euo pipefail

# See https://blastedbio.blogspot.co.uk/2016/05/sync-github-mirror-with-cron.html and
# https://gist.github.com/peterjc/eccac1942a9709993040425d33680352 for mirroring script
#
# Usage:
#
# 1. Fork upstream repo under HuttonICS, disable wiki, projects, issues etc. Protect master branch.
# 2. Run:

peterjc

#!/usr/bin/env python
# Copyright 2021-2024 by Peter Cock, The James Hutton Institute.
# All rights reserved.
# This file is released under the "MIT License Agreement".
"""Python script to keep GitHub mirrors in sync with upstream.

Mirror mirror on the wall, who's the newest of them all?

Usage:

peterjc

#!/bin/bash

# Enable strict bash mode - halts on any error
set -euo pipefail

# Takes exactly three command line arguments:
git_dir=$1
ssh_key=$2
log_file=$3

peterjc

peterjc

Keybase proof

I hereby claim:

• I am peterjc on github.
• I am pjacock (https://keybase.io/pjacock) on keybase.
• I have a public key ASDyMh8PfhtgajUDmucW2sUhci9kIZ5U2TywiDd5GKUlyAo

To claim this, I am signing this object:

peterjc

#!/usr/bin/env python
#Copyright 2013, Peter Cock. All rights reserved.
#Released under the MIT License.
"""Python scipt to generate Roomba IR codes for LIRC.
 
Tested under Python 2.7 and Python 3.3, example usage:

$ python make_roomba_lirc.py > roomba.conf

See also:

peterjc

# Copyright 2016 Peter Cock, James Hutton Institute.
# All Rights Reserved.
# Released as open source under the MIT license.
"""Update URLs in Galaxy tool_dependencies.xml files

Assumes have a copy of the urls.tsv file from
https://github.com/galaxyproject/cargo-port/blob/master/urls.tsv

This file defines the https://depot.galaxyproject.org/software/
URL naming used for caching Galaxy dependencies.

peterjc

from reportlab.pdfgen import canvas
from reportlab.lib.pagesizes import letter
from reportlab.lib.units import inch
from reportlab.lib import colors
from reportlab.pdfbase.pdfmetrics import stringWidth

from reportlab.graphics.shapes import Drawing, String, Line, Rect, Wedge, ArcPath
from reportlab.graphics import renderPDF, renderPS
from reportlab.graphics.widgetbase import Widget

peterjc

#!/usr/bin/env python 
#Copyright 2013, Peter Cock. All rights reserved.
#Released under the MIT License.
"""Python scipt to decode Roomba IR codes via the Linux mode2 tool.

Tested under Python 2.7 and Python 3.3, example usage:

$ mode2 -d /dev/lirc0 | python decode_roomba_ir.py
10101100 - 172 - 0xAC
10101100 - 172 - 0xAC

peterjc

#!/usr/bin/env python
#Example usage:
#
#    $ python ace_to_contig_stats.py < example.ace > example_stats.tsv
#
import sys
from Bio.Sequencing import Ace

sys.stdout.write("#Contig\tPadded length\tUnpadded length\tReads\n")
for contig in Ace.parse(sys.stdin):