ksuderman

Every time I want to import an existing project into GitHub I have to Google for the instructions. Hopefully this gist will be easier for me to find...

1. Create a new repository on GitHub and make note of the URL. The URL will be something like https://github/ksuderman/org.anc.some.project.git (don't forget the .git extension).
2. CD to the root on your project source code.
3. git init
4. git add . (or explicityly specify directories and files to be added).
5. git commit -m "Initial code import."
6. git remote add origin [URL] (where [URL] is the URL from step one)
7. git pull origin master
8. git push origin master

ksuderman

# See http://stackoverflow.com/questions/59895/getting-the-source-directory-of-a-bash-script-from-within
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
  DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
  SOURCE="$(readlink "$SOURCE")"
  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"

ksuderman

secret=`cat /dev/urandom | tr -dc _A-Z-a-z-0-9 | head -c${1:-16};echo;`
echo $secret

# If tr complains about illegal byte sequences it is because tr can not handle UTF-8 characters.
# The solution is to specify the C locale for tr
secret=`cat /dev/urandom | LC_ALL=C tr -dc _A-Z-a-z-0-9 | head -c${1:-16};echo;`
echo $secret

ksuderman

{
  "embeddings": [
    {
      "tensorName": "Covid-19 Dataset",
      "tensorShape": [
        1000,
        50
      ],
      "tensorPath": "https://www.lappsgrid.org/tensors/model300_5_5_50_cbow_abs_intro.tsv",
      "metadataPath": "https://www.lappsgrid.org/tensors/metadata.txt"

ksuderman

tools:
- name: sra_tools
  owner: iuc
  revisions:
  - f5ea3ce9b9b0
  - e08a7ad4378b
  tool_panel_section_label: Get Data
  tool_shed_url: toolshed.g2.bx.psu.edu
- name: ncbi_acc_download
  owner: iuc

ksuderman

#!/bin/bash
# gxadmin: Galaxy administration swiss army knife
# license: GPLv3
#
# This is the result of admins across the universe working together :)
#
# Thanks to everyone for their contributions
# https://github.com/galaxyproject/gxadmin/graphs/contributors
version() {
	echo 19

ksuderman

"""
This script is loosely based on https://github.com/galaxyproject/bioblend/blob/main/docs/examples/run_imported_workflow.py

TO-DO
1. Allow the user to specify an output history.
2. Maybe allow the user to specify a URL to data that should be uploaded to
   the server to be used as input to the workflow.
3. Don't assume the name of the input parameter is 'input'

usage: workflows.py [-h] [-s SERVER] [-a API_KEY] -w WORKFLOW -d DATASET

ksuderman

#!/usr/bin/env bash

# Use this script to update the GalaxyKubeman Helm chart versions in Leo
#
# Put this script on your path and run from the root Leonardo source directory.
# > cd /home/user/leonardo
# 
# USAGE
#   > bumpleo <new version>
#

ksuderman

# ANSI color codes for the console.
reset="\033[0m"
bold="\033[1m"
ital="\033[3m" # does not work on OS X

# Function used to highlight text.
function hi() {
    echo -e "$bold$@$reset"
}

ksuderman