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Björn Grüning bgruening

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bgruening / university_refuguess_help.md
Last active October 5, 2015 21:18
Ideas how a university can help refugees

Sehr geehrter Herr Redl,

bezugnehmend auf die Refugees Mail vom Rektor hier ein paar Ideen von der Plenumssitzung der Gruppe Rieselfeld.

Im Grunde gibt es 3 Themen bei denen die vielen Freiwilligen Hilfe bräuchten und die Uni als größter Arbeitgeber und als Integrationseinrichtung Nummer 1 in Freiburg einen entscheidenden Beitrag leisten könnte und sollte.

  1. Zugang zu Infrastruktur

Räume, Sportplätze, Computerräume. Eine zentrale Anlaufstelle für solche Sachen würde sehr helfen. Die vielen Freiwilligen Helfer wissen

@bgruening
bgruening / first_class_postgresql_galaxy_integration.md
Last active November 9, 2015 18:21
postgresql/mysql Galaxy integration as tool and visualisation

First class postgresql/mysql Galaxy integration

With this document I try to struture my ideas about a solid postgresql/mysql integration in Galaxy as part of out GIE work and beyond.

A lot of tools relying on ORDBMS for storing and quering data. This is not so common in NGS or proteomics but it is in cheminformatics, text-minining and genome annotation. See for example blast2GO which uses a mysql database as backend, or the ChemicalToolBox for storing the entire PubChem in a phchem indexed postgresql backend. In general I think it makes sense to support ORDBMS in Galaxy if data do not change

@bgruening
bgruening / iuc_codefest_summary_002.md
Last active December 9, 2015 21:07
Second IUC codefest summary

The Intergalactic Utilities Commission was organising it's second codefest with the aim to improve metagenomic research in Galaxy.

The IUC was available for two days in a Hangout to answers questions and to work together with the Galaxy community to enhance our tools and the overall Galaxy ecosystem. 22 scientists from all over the world participated in this and made it a fantastic experience and a success story, which the IUC would like to repeat more often.

  • Bérénice Batut (CIDAM Université Auvergne)
  • Laura Leroi (Ifremer)
@bgruening
bgruening / rfc_download_by_proxy.md
Last active January 1, 2016 13:09
RFC: download_by_proxy action type

This is a RFC to get the implementation details right for a new action type in tool_dependencies.xml.

Since years we try to save a very crucial sustainability problem: Non-sustainable links!

A little bit of history

At first we tried to mirror tarballs with sceptical sustainability, like BioC or random FTP servers. But over time we encountered many more places which we can not trust. Google-Code, SourceForge etc ...

@bgruening
bgruening / core.galaxy_ui.yaml
Last active January 5, 2016 22:27
Galaxy Userinterface Tour
id: galaxy_ui
name: Galaxy UI
description: A gentle introduction to the Galaxy User Interface
title_default: "Welcome to Galaxy"
# A tour is made of several steps, each of them beginning with a dahs '-'
steps:
# 'title's will be displayed in the header of each step-container
# If you don't specify any title, a default title is used, defined above.
- title: "Welcome to Galaxy"
@bgruening
bgruening / galaxy_rt_comm.md
Last active June 4, 2016 11:44
Galaxy real-time communication server

Galaxy with real-time communication skills

Check out this branch: https://github.com/bgruening/galaxy/tree/rt_comm

Install some requirements into Galaxy's virtualenv:

. GALAXY_ROOT/.venv/bin/activate
pip install flask flask-socketio eventlet
@bgruening
bgruening / galaxy-fr-newsletter-june.md
Last active June 7, 2016 06:11

Galaxy June update

Welcome to our Galaxy Freiburg newsletter. A lot of new features have been included in the Galaxy framework with the new 16.04 release. Furthermore, we integrated a bunch of new tools and updated the others. Big thanks to the entire Galaxy community which makes this happen! As usual we are happy to take questions on various channels. For more information please read the community section.

New Galaxy features

@bgruening
bgruening / galaxy-communication-server.md
Last active June 19, 2016 20:08
RFC: Galaxy Communication Server

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.

@bgruening
bgruening / galaxyp_conda_contribution_fest.md
Created September 30, 2016 06:34
GalaxyP Conda Contribution Fest

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 / docker_involucro.md
Last active October 7, 2016 20:44
Build Docker container the involucro way with Conda packages

Building Docker containers with involucro for local Conda packages

install galaxy-lib

conda install galaxy-lib -c bioconda

build your recipe