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

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

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

# 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

#!/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

#
# A hack, loosly based on Eric Rasche's disgusting.py
# https://gist.github.com/erasche/4ac3448b036f09979e14
#
# Intended as a one-off use script to help with syncing local
# .shed.yml files with a Galaxy Tool Shed. See also:
# https://gist.github.com/peterjc/5ebbf446d799f3aaa639

import yaml
import os

peterjc

from Bio import SeqIO
with open("CP008802.txt", "w") as output:
    output.write("Seqname\tSource\tfeature\tStart\tEnd\tScore\tStrand\tFrame\tAttributes\n")
    for record in SeqIO.parse("CP008802.gbk", "genbank"):
        print("Converting %s" % record.name)
        for f in record.features:
            if f.type != "gene":
                continue
            locus_tag = f.qualifiers["locus_tag"][0]
            if len(f.location.parts) > 1:

peterjc

# Walks specified folders looking for .shed.yml files,
# with at least owner and name given.
#
# Matches the owner/name with the remote Tool Shed, and
# takes any missing meta-data from the remote Tool Shed.
#
# Pre-existing local data otherwise should be preserved.
#
# Does the yaml dump with some hackery because I couldn't
# work out how to make the library use the layout I wanted.

peterjc

#!/usr/bin/env python
"""Galaxy Tool Shed diff command."""

import sys
import os
import subprocess
import tempfile
from optparse import OptionParser

VERSION = "v0.0.1"