Skip to content

Instantly share code, notes, and snippets.

View mtekman's full-sized avatar

mtekman mtekman

42 followers · 44 following
  • University Freiburg
  • Freiburg, DE
View GitHub Profile
@mtekman
mtekman / galaxy_download_datasets.py
Last active October 8, 2020 16:17
Galaxy Download Scripts
#!/usr/bin/env python3
__VERSION__ = "0.3"
'''This script downloads datasets from public or user histories, using
a variety of different strategies, namely:
* If the user provides an URL: Either import the history, or select
it publicly (but with restricted access, i.e. slow dataset matching)
* If the user provides a title: Either select one from the user's list,
@mtekman
mtekman / debug-galaxy-history.org
Last active October 25, 2020 22:24
How to Debug a Red Error Dataset
@mtekman
mtekman / headphones.org
Last active October 30, 2020 10:13
Headphones for Home Office

This gist has migrated to GitLab

https://gitlab.com/mtekman/work-snippets

(The copy here is archived. Please see the above link for the latest developments)
NamesCost(€)QualityComfortNoise CancellingLinkNotes
Sony WH-1000XM3249GreatGoodActive. GreatHereBest of last generation. New version XM4 is available for +100 € more and a 10% noise-cancelling quality increase.
Microsoft Surface 2249GoodGoodActive. Good[[https://www.amazon.de/s?k=microsoft+surface+2+headphones&crid=2O2XD5TLQB5AW&sprefix=microsoft+surface+2%2Caps%2C161&r
@mtekman
mtekman / starsolo.org
Last active October 25, 2020 22:22
Subsetting STARsolo data for Galaxy testing
@mtekman
mtekman / galaxy-promo-video.org
Last active October 25, 2020 22:25
Automated mouse and keyboard events for a Galaxy intro video for scRNA-seq
@mtekman
mtekman / xunit.org
Last active October 25, 2020 22:25
Galaxy xUnit Errors
@mtekman
mtekman / funding.org
Last active October 25, 2020 22:31
Funding Bodies

This gist has migrated to GitLab

https://gitlab.com/mtekman/work-snippets

(The copy here is archived. Please see the above link for the latest developments)

Funding

PAUSED Looking at Funding bodies for short term

@mtekman
mtekman / setting-up-galaxy.org
Last active October 25, 2020 22:26
How to set up a Galaxy Development environment (as a VM or other)

Setting Up A Working Galaxy Environment

This gist has migrated to GitLab

https://gitlab.com/mtekman/galaxy-snippets

(The copy here is archived. Please see the above link for the latest developments)

TL;DR: Clone tools-iuc, use Ubuntu 18.04 LTS, and follow the official planemo instructions to get a working Galaxy installation. Otherwise continue below.

@mtekman
mtekman / conf.org
Last active November 22, 2020 23:58
Configs (single-file dotfiles using org-mode)
  • Global public configs for multiple utils. Makes use of tangled files.
  • C-c C-v t to export all.

First Run

Nix System

@mtekman
mtekman / config
Last active March 18, 2019 12:01
i3 config
# This file has been auto-generated by i3-config-wizard(1).
# It will not be overwritten, so edit it as you like.
#
# Should you change your keyboard layout some time, delete
# this file and re-run i3-config-wizard(1).
#
# i3 config file (v4)
#
# Please see https://i3wm.org/docs/userguide.html for a complete reference!