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View pgp_pilot_library_info.yaml
---
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:
@bgruening
bgruening / mercurial_fix_merge_conflicts.md
Created May 5, 2019
mercurial (hg) resolve merge conflicts by accepting upstream changes
View mercurial_fix_merge_conflicts.md

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

View gist:b1bdb33800ad6efea474b63bedfa96c6
* 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
View gist:b4f7b33f886a064715ad00a9b7ea3bd6
> 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
@bgruening
bgruening / get_all_containers.py
Created Jan 23, 2017
get all biocontainers via Quay.io API
View get_all_containers.py
#!/usr/bin/env python
import argparse
import json
import sys
import tempfile
try:
import requests
except ImportError:
@bgruening
bgruening / biocontainers_stats_01_2017.md
Last active Jan 23, 2017
BioContainers stats January 2017
View biocontainers_stats_01_2017.md
  • 263 GB
  • 2598 overall Images
  • 332 Perl Images
  • 666 R Images (!BioC)
  • 266 BioConductor Images
  • 817 Python Images
@bgruening
bgruening / docker_involucro.md
Last active Oct 7, 2016
Build Docker container the involucro way with Conda packages
View docker_involucro.md

Building Docker containers with involucro for local Conda packages

install galaxy-lib

conda install galaxy-lib -c bioconda

build your recipe

@bgruening
bgruening / galaxyp_conda_contribution_fest.md
Created Sep 30, 2016
GalaxyP Conda Contribution Fest
View galaxyp_conda_contribution_fest.md

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)
@bgruening
bgruening / GTN.md
Last active Oct 17, 2016
GTN - new shared training material and technologies for training!
View GTN.md

Dear training enthusiast,

We have started to work on an unification of the Galaxy training material as discussed during the GCC 2016. As a first example we have chosen our Exome-Seq tutorial and have ported it over to give a real world example of how we imagine the next generation of Galaxy training looks like. Look by yourself: https://github.com/bgruening/training-material/tree/master/Exome-Seq

A few highlights

  • Slides are written in reveal.js
@bgruening
bgruening / galaxy-communication-server.md
Last active Jun 19, 2016
RFC: Galaxy Communication Server
View galaxy-communication-server.md

Realtime communication server and its user-interface

Galaxy makes it very easy to analyse data but communicating with other researchers and sharing tricks or asking questions is too hard and a for many people big hurdle.

We should promote https://biostar.usegalaxy.org wherever we can, but I think there is also a need for quick, instant help ... like we (developers) do with IRC.

This PR integrates a realtime communication server and it's user-interface.

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