sschmeier

channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - pandas
  - pyfaidx
  - pysam==0.15.4
  - pybedtools
  - pip:

sschmeier

Fix tmux messing with conda

Problem: When running a conda environment and opening tmux on macOS, a utility called path_helper is run again. Essentially, the shell is initialized twice which messes up the ${PATH} so that the wrong Python version shows up within tmux.

Solution

If using bash, edit /etc/profile and add one line. (For zsh, edit /etc/zprofile)

...

sschmeier

Private fork on GitLab

Aim

Have a public repo on github for the world to see + have a the same repo private on gitlab for project specific branches/dev. Locally use github as upstream and gitlab as origin. We develop in gitlab and push general applicable changes to our upstream github repo.

In detail:

1. one for our private repository on gitlab (will be the default one, called origin)
2. one to be connected to a repo on github, to be able to publish new general changes (will be called upstream)

sschmeier

#!/usr/bin/env python
import sys, subprocess, requests

def msg2slack(msg, channel, user):
    url = "<URL>" # your Slack incomming webhook url 
    payload = {"channel": '#%s' % channel,
               "username": user,
               "text": msg,
               "icon_emoji": ":computer:"}
    r = requests.post(url, json=payload)

sschmeier

# Edit this file to introduce tasks to be run by cron.
#
# Each task to run has to be defined through a single line
# indicating with different fields when the task will be run
# and what command to run for the task
#
# To define the time you can provide concrete values for
# minute (m), hour (h), day of month (dom), month (mon),
# and day of week (dow) or use '*' in these fields (for 'any').#
# Notice that tasks will be started based on the cron's system