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Björn Grüning bgruening

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University of Freiburg
Freiburg (Germany)
orcid.org/0000-0002-3079-6586

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Popular repositories

docker-galaxy-stable Public

🐳📊📚 Docker Images tracking the stable Galaxy releases.

Shell 202 133
galaxytools Public

🔬📚 Galaxy Tool wrappers

HTML 98 179
awesome-ukraine-support Public

A list of resources and inititive to help the Ukraine

46 14
conda_r_skeleton_helper Public

Cleaning up Conda r-packages

Python 41 23
galaxy-rna-workbench Public

Galaxy RNA workbench

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galaxy-ipython Public

🔬📚 IPython Integration into Galaxy

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3,700 contributions in the last year

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Activity overview

Contributed to usegalaxy-eu/website, galaxyproject/tools-iuc, BioContainers/multi-package-containers and 106 other repositories

Contribution activity

June 2022

Created 69 commits in 11 repositories

Created a pull request in galaxyproject/galaxy that received 3 comments

Fix the swift integration tests that are using some minio container

The minio container yields an error with /tmp/data. Maybe that fixes the integration tests? bag@bag:~$ docker run -p 9000:9000 -i -t minio/minio:la…

+1 −1 • 3 comments

Opened 4 other pull requests in 4 repositories

usegalaxy-eu/infrastructure-playbook 1 merged

disable database_engine_option_server_side_cursors Jun 24

usegalaxy-eu/website 1 merged

Create 2022-06-23-Repurposing-COVID-19-pipelines-for-the-monkeypox-vi… Jun 23

bioconda/bioconda-recipes 1 open

try a rebuild of concoct Jun 17

galaxyproject/tools-iuc 1 merged

fix tool version requirement in goseq Jun 3

Reviewed 89 pull requests in 10 repositories

galaxyproject/tools-iuc 24 pull requests

kc-align fix number of threads Jun 24
Update to merqury tool wrapper Jun 23
Add new tool SynDiva Jun 23
Use 7z to decompress ncbi_datasets archives Jun 23
ragtag: symlink input fasta files Jun 23
spyboat: allow 1 line difference in output Jun 23
nanocompore: symlink reference Jun 23
anndata export: open loompy file read only Jun 21
cutadapt: fix test Jun 21
MaxBin2: Modify reads/abunds to use repeat instead of multiple to support using collection Jun 17
Update mlst to 2.22.0 Jun 15
Update prot-scriber to v.0.1.3 Jun 15
CONCOCT: Update versions, replace scripts and tests Jun 14
Update pyega3.xml: missing --start Jun 14
Mitos2: mising genes output Jun 12
Add yahs tool Jun 12
Upgrade vSNP tools to version 3 Jun 10
Updating tools/spaln from version 2.4.7 to 2.4.9 Jun 9
Don't include genomic cds and rna fasta files in genomic fasta collec… Jun 7
Seqcomplexity Jun 7
Updating tools/purge_dups from version 1.2.5 to 1.2.6 Jun 6
Produce nested collection for ncbi_datasets genome_fasta output Jun 2
Meryl: fix output trio mode Jun 2
Add seqkit stats and fx2tab tools Jun 1

bioconda/bioconda-recipes 23 pull requests

Update downloading and handling of dependencies in MetaNovo recipe Jun 23
pypgatk version 0.0.22 Jun 23
Add r-geneexpressionfromgeo. Jun 22
Update fiji Jun 16
Update entrez-direct recipe to use extended-base Jun 14
Update prot-scriber to 0.1.3 Jun 14
Install_miga_v1.0.0 Jun 11
Update PlasmidFinder for better container support Jun 10
Update thermorawfileparser to 1.4.0 Jun 10
Update chipseeker v.1.32.0 Jun 9
Update meta.yaml Jun 7
Update meta.yaml of StrainScan V1.0.10 Jun 7
Update cgranges for Python 3.6 Jun 6
Update pcaone Jun 5
Update sam2lca python version to 3.7 Jun 5
Update deepvariant to 1.4.0 Jun 5
Update abritamr to 1.0.8 Jun 5
Update perl-text-balanced to 2.06 Jun 5
Update metapi to 2.1.4 Jun 5
Update gffutils to 0.11.0 Jun 5
Update r-restfulr to 0.0.14 Jun 5
Update r-dartr to 2.0.4 Jun 5
Update ViennaRNA Package to upstream version 2.5.1 Jun 5

galaxyproject/galaxy 16 pull requests

[22.05] Switch History Modal: fix pagination Jun 24
[22.05] Fix showing invocations for a particular workflow. Jun 17
Storage Dashboard: fix unlimited quota display Jun 17
Remove fabric as a dependency for Galaxy. Jun 7
Support phylocanvas autobuild Jun 7
Fix jest test warnings for saved rules and markdown test Jun 5
Fix a small error in job doc Jun 3
Refactor uses_shed.py so test_base doesn't depend on galaxy-app. Jun 3
Small tour tweaks. Jun 3
More workflow Jest tests. Jun 3
Implement initial GA4GH DRS Support. Jun 3
Script to validate tours structure. Jun 3
Drop update_time from JobStateHistory Jun 2
Workflow deletion selenium tests. Jun 2
Remove can_eliminate_tool_dependency from tool shed code. Jun 1
Localize workflow deletion confirmation message... Jun 1

usegalaxy-eu/website 6 pull requests

BioContainers/multi-package-containers 5 pull requests

bgruening/galaxytools 5 pull requests

Update PharmCAT to 1.8 Jun 14
Update Chipseeker v.1.32.0 Jun 9
RiboTaper: fix indexed genome input Jun 7
Update ribotaper Jun 3
Update gfastats: v.1.2.2 Jun 1

usegalaxy-eu/usegalaxy-eu-tools 4 pull requests

add syndiva tools to iuc yaml Jun 24
Add Smudgeplot and Cactus Jun 21
add prot-scriber iuc tool Jun 14
Add a new tools 10x_bamtofastq to Single-cell section Jun 3

galaxyproject/training-material 3 pull requests

Fix an error in Galaxy 101 tutorial Jun 18
Auto Compress Images Jun 6
Fix minor typos Jun 2

galaxyproteomics/tools-galaxyp 2 pull requests

suite_mqppep addition to tools-galaxyp Jun 20
bump eggnog Jun 20

bioconda/bioconda-utils 1 pull request

feat: update mulled-test conda to 4.12 Jun 21

Created an issue in galaxyproject/galaxy that received 7 comments

Slow tool form building on EU (for certain histories)

On EU the tool form build can be really slow. Up to minutes. We investigated this during the last days and could drill it down to: it only affects…

7 comments

Opened 8 other issues in 5 repositories

galaxyproject/galaxy 2 open 1 closed

usegalaxy-eu/website 2 open

wolfgangs talk at the ELIXIR cancer data focused group Jun 17
ELIXIR AHM summary Jun 10

usegalaxy-au/infrastructure-playbooks 1 open

enable TRS workflow endpoint on usegalaxy.org.au Jun 10

galaxyproject/tools-iuc 1 open

snipit as Galaxy tool Jun 3

galaxyproject/galaxy-hub 1 open

https://galaxyproject.org/projects/ should not be a 404 Jun 3

2 contributions in private repositories Jun 7 – Jun 13