Björn Grüning bgruening

GalaxyP Conda Contribution Fest

On September 27th and 28th, the Galaxy-P project organized it's first Contribution fest with the aim to port as many as possible tool dependencies to Conda packages. Conda packages are the future of Galaxy’s tool dependency management and will yield more robust tools and automatic CI testing of all Galaxy-P tools.

The Galaxy-P community was available for two days on gitter and helped everyone who wanted to contribute and to get started with Conda packaging. Thanks to all contributors for their amazing work, the priceless french lessons and all the fun we had discovering all the pitfalls of packaging scientific software.

Matt Chambers (Vanderbilt University)

Building Docker containers with `involucro` for local Conda packages

install galaxy-lib

conda install galaxy-lib -c bioconda

build your recipe

263 GB
2598 overall Images
332 Perl Images
666 R Images (!BioC)
266 BioConductor Images
817 Python Images

~/venv/bin/hg resolve -t internal:other --all

(please click the badges they should work 😃)

Badges to run workflows on usegalaxy.eu imported from workflowhub.eu

[![Run Workflow](https://img.shields.io/badge/run%20workflow%20-usegalaxy.eu-brightgreen?logo=data:image/png;base64,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

	#!/usr/bin/env python

	import argparse
	import json
	import sys
	import tempfile

	try:
	import requests
	except ImportError:

	> grep galaxy.workflow.run handler0.log \| tail -n 400
	galaxy.workflow.run DEBUG 2017-03-26 09:34:44,527 Workflow step 119445 of invocation 22697 delayed (8.096 ms)
	galaxy.workflow.run DEBUG 2017-03-26 09:34:44,529 Workflow step 119446 of invocation 22697 delayed (1.118 ms)
	galaxy.workflow.run DEBUG 2017-03-26 09:34:44,533 Workflow step 119439 of invocation 22697 delayed (2.844 ms)
	galaxy.workflow.run DEBUG 2017-03-26 09:34:44,534 Workflow step 119440 of invocation 22697 delayed (1.142 ms)
	galaxy.workflow.run DEBUG 2017-03-26 09:34:44,535 Workflow step 119441 of invocation 22697 delayed (0.544 ms)
	galaxy.workflow.run DEBUG 2017-03-26 09:34:44,537 Workflow step 119442 of invocation 22697 delayed (0.666 ms)
	galaxy.workflow.run DEBUG 2017-03-26 09:34:44,541 Workflow step 119443 of invocation 22697 delayed (0.587 ms)
	galaxy.workflow.run DEBUG 2017-03-26 09:34:44,542 Workflow step 119448 of invocation 22697 delayed (0.541 ms)
	galaxy.workflow.run DEBUG 2017-03-26 09:34:44,543 Workflow step 119447 of invocation 22697

	* galaxy
	* https://github.com/bgruening/docker-galaxy-ngs-preprocessing
	* https://github.com/bgruening/galaxy-rna-seq
	* https://github.com/bgruening/galaxy-rna-structural-analysis
	* https://github.com/bgruening/galaxy-rna-workbench
	* https://github.com/bgruening/docker-galaxy-exome-seq/pull/15
	* https://github.com/bgruening/docker-galaxy-epigenetics
	* https://github.com/bgruening/docker-galaxy-phylogenetics
	* https://github.com/bgruening/docker-recipes/blob/master/galaxy-deeptools
	* https://github.com/shiltemann/galaxy-metagenomics

	---
	destination:
	type: library
	name: 'PGP-UK Open Access Data'
	description: 'Open Access Genomic, Transcriptomic and Methylomic Data from the Personal
	Genome Project UK. DOI: 10.1186/s12920-018-0423-1'
	items:
	- name: Genetic Data (WGS)
	description: Open access WGS data from the PGP-UK Project
	items: