(please click the badges they should work 😃)
Björn Grüning bgruening
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bgruening
/ pgp_pilot_library_info.yaml
Created
October 14, 2019 14:34
— forked from IsmailM/pgp_pilot_library_info.yaml
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| --- | |
| 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
/ mercurial_fix_merge_conflicts.md
Created
May 5, 2019 18:42
mercurial (hg) resolve merge conflicts by accepting upstream changes
~/venv/bin/hg resolve -t internal:other --all
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| * 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 |
bgruening
/ gist:b4f7b33f886a064715ad00a9b7ea3bd6
Created
March 27, 2017 20:08
workflow_incovation_log_for_john
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| > 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
/ get_all_containers.py
Created
January 23, 2017 19:47
get all biocontainers via Quay.io API
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| #!/usr/bin/env python | |
| import argparse | |
| import json | |
| import sys | |
| import tempfile | |
| try: | |
| import requests | |
| except ImportError: |
bgruening
/ biocontainers_stats_01_2017.md
Last active
January 23, 2017 19:37
BioContainers stats January 2017
- 263 GB
- 2598 overall Images
- 332 Perl Images
- 666 R Images (!BioC)
- 266 BioConductor Images
- 817 Python Images
bgruening
/ docker_involucro.md
Last active
October 7, 2016 20:44
Build Docker container the involucro way with Conda packages
bgruening
/ galaxyp_conda_contribution_fest.md
Created
September 30, 2016 06:34
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)
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
- Slides are written in reveal.js
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