A --log-handler-script log script for snakemake that pushes the status to Slack

log_handler_slack.py

# License: MIT

import socket
from slacker import Slacker
import datetime
import time
import threading

SLACK_TOKEN = 'xoxb-00000000000-000000000000-000000000000000000000000'
CHANNEL_NAME = "your-channel-on-slack"

hostname = socket.gethostname()
prefix = "Snakemake is running on {}\n".format(hostname)

slack = Slacker(SLACK_TOKEN)
last_message = "Snakemake just started"

res = slack.chat.post_message(CHANNEL_NAME, last_message, as_user=True)
msg_ts = res.body['ts']
channel_id = res.body['channel']

def new_message(msg):
    global last_message
    last_message = msg

def update_message():
    slack.chat.update(channel_id, msg_ts, prefix + last_message + "\nLast update at: {}".format(datetime.datetime.now().strftime("%d/%m %H:%M:%S")))

def get_bar(current, total, size=20):
     nb_to_display = int(size * current / total)
     return ("\u26AB" * nb_to_display) + ("\u26AA" * (size - nb_to_display))

def log_handler(msg):
    if msg.get('level') == 'progress':
        cur = msg['done']
        total = msg['total']
        new_message(get_bar(cur, total) + " {}/{}".format(cur, total))

def update_slack():
    while True:
        update_message()
        time.sleep(2)

update_message()
d = threading.Thread(name='slack-daemon', target=update_slack)
d.setDaemon(True) # the thread will close itself when snakemake shuts down
d.start()