Acanthophis
Acanthophis: a comprehensive plant hologenomics pipeline - Published in JOSS (2024)
Science Score: 98.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README and JOSS metadata -
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Links to: joss.theoj.org -
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✓JOSS paper metadata
Published in Journal of Open Source Software
Scientific Fields
Repository
A comprehensive, opinionated plant metagenomics and variant calling pipeline in Snakemake
Basic Info
Statistics
- Stars: 7
- Watchers: 1
- Forks: 2
- Open Issues: 1
- Releases: 10
Metadata Files
README.md
Acanthophis
A reusable, comprehensive, opinionated Snakemake pipeline for plant-microbe genomics and plant variant calling.
Documentation
For documentation, see ./documentation.md. In summary:
```bash
create conda env, activate it
mamba create -n someproject python snakemake pip natsort mamba activate someproject
Install acanthophis itself
pip install acanthophis
Generate a workspace. This copies all files the workflow will need to your
workspace directory.
acanthophis-init /path/to/someproject/
Edit config.yml to suit your project. Hopefully this config file documents
all options available in an understandable fashion. If not, please raise an
issue on github.
vim config.yml
Run snakemake
snakemake -j 16 -p --use-conda --conda-frontend mamba --ri
Or on a cluster, see acanthophis-init --list-available-profiles
snakemake --profile ./ebio-cluster/ ```
Compatibility
While snakemake and Acanthophis are cross-platform, most of the underlying tools are only packaged for and/or only operate on Linux x68_64. Therefore, I only support users on Linux systems. In theory, everything should run on OSX or WSL, but the vast majority of users will want to utilise a high performance linux workstation (at least, probably more likely a cluster).
Running tests
For running tests, see ./tests/README.md.
Contribution & Assistance
If you have anything (advice, docs, code) you'd like to contribute, pull requests are more than welcome. Please discuss any major contribution in a new issue before implementing it, to avoid wasted effort.
If you need any assistance, or have other questions or comments, please make an issue on github, or open a discussion. Unfortunately both need an account on github, so alternatively you can email me (foss <usual email symbol> kdmurray.id.au).
About & Authors
This is an amalgamation of several pipelines developed between the Weigel Group, MPI DB, Tübingen, DE, the Warthmann Group, IAEA/FAO PBGL, Seibersdorf, AT and the Borevitz Group, ANU, Canberra, AU. This amalgamation authored by Dr. K. D. Murray, original code primary by K. D. Murray, Norman Warthmann, with contributions from others at the aforementioned institutes.
Owner
- Name: Dr. K. D. Murray
- Login: kdm9
- Kind: user
- Location: Tübingen, DE
- Company: Max Planck Institut für Entwicklungsbiologie, Tübingen
- Website: https://kdmurray.id.au
- Repositories: 100
- Profile: https://github.com/kdm9
Hacking on DNA
JOSS Publication
Acanthophis: a comprehensive plant hologenomics pipeline
Authors
Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
Research School of Biology, Australian National University, Canberra, Australia
Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
Research School of Biology, Australian National University, Canberra, Australia, FAO/IAEA Joint Centre of Nuclear Techniques in Food and Agriculture, Plant Breeding and Genetics Laboratory, Seibersdorf, Austria
Editor
Marcos Vital
Tags
python snakemake plants metagenomics variant calling population genomics reference-free classificationCitation (CITATION.cff)
cff-version: "1.2.0"
authors:
- email: kdmpapers@gmail.com
family-names: Murray
given-names: Kevin D.
orcid: "https://orcid.org/0000-0002-2466-1917"
- family-names: Borevitz
given-names: Justin O.
orcid: "https://orcid.org/0000-0001-8408-3699"
- family-names: Weigel
given-names: Detlef
orcid: "https://orcid.org/0000-0002-2114-7963"
- family-names: Warthmann
given-names: Norman
orcid: "https://orcid.org/0000-0002-1178-8409"
contact:
- email: kdmpapers@gmail.com
family-names: Murray
given-names: Kevin D.
orcid: "https://orcid.org/0000-0002-2466-1917"
- family-names: Warthmann
given-names: Norman
orcid: "https://orcid.org/0000-0002-1178-8409"
doi: 10.5281/zenodo.10795245
message: If you use this software, please cite our article in the
Journal of Open Source Software.
preferred-citation:
authors:
- email: kdmpapers@gmail.com
family-names: Murray
given-names: Kevin D.
orcid: "https://orcid.org/0000-0002-2466-1917"
- family-names: Borevitz
given-names: Justin O.
orcid: "https://orcid.org/0000-0001-8408-3699"
- family-names: Weigel
given-names: Detlef
orcid: "https://orcid.org/0000-0002-2114-7963"
- family-names: Warthmann
given-names: Norman
orcid: "https://orcid.org/0000-0002-1178-8409"
date-published: 2024-03-25
doi: 10.21105/joss.06062
issn: 2475-9066
issue: 95
journal: Journal of Open Source Software
publisher:
name: Open Journals
start: 6062
title: "Acanthophis: a comprehensive plant hologenomics pipeline"
type: article
url: "https://joss.theoj.org/papers/10.21105/joss.06062"
volume: 9
title: "Acanthophis: a comprehensive plant hologenomics pipeline"
GitHub Events
Total
- Push event: 1
Last Year
- Push event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Dr. K.D. Murray | f****s@k****u | 279 |
| Brice Letcher | b****r@e****r | 3 |
| Juanjo Bazán | j****n@g****m | 1 |
| George Bouras | 8****3 | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 16
- Total pull requests: 5
- Average time to close issues: 3 months
- Average time to close pull requests: 1 day
- Total issue authors: 4
- Total pull request authors: 4
- Average comments per issue: 2.69
- Average comments per pull request: 0.4
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- gbouras13 (7)
- kdm9 (5)
- bricoletc (3)
- abhishektiwari (1)
Pull Request Authors
- bricoletc (3)
- gbouras13 (2)
- kdm9 (1)
- xuanxu (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 331 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 19
- Total maintainers: 1
pypi.org: acanthophis
A comprehensive, opinionated plant variant calling pipeline in Snakemake
- Homepage: https://github.com/kdm9/acanthophis
- Documentation: https://acanthophis.readthedocs.io/
- License: Mozilla Public License 2.0 (MPL 2.0)
-
Latest release: 1.1.0
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite
- pypa/gh-action-pypi-publish release/v1 composite
- pypa/gh-action-pypi-publish master composite
- actions/cache v3 composite
- actions/checkout v3 composite
- conda-incubator/setup-miniconda v2 composite
- condaforge/mambaforge latest build
- actions/checkout v3 composite
- actions/upload-artifact v1 composite
- openjournals/openjournals-draft-action master composite