<p align="center">
<a href="https://hydra-genetics.readthedocs.io">https://hydra-genetics.readthedocs.io</a>
</p>
# <img src="images/hydragenetics.png" width=40 /> Hydra-genetics
Command line interface to create new modules/pipelines or adding a new rule to an existing project. Provides libraries used to make it easier for people not used to pandas to extract information from samples and units dataframes. These dataframes are generated from [units.tsv](https://github.com/hydra-genetics/tools/blob/develop/hydra_genetics/pipeline-template/workflow/schemas/units.schema.yaml) and [samples.tsv](https://github.com/hydra-genetics/prealignment/blob/develop/workflow/schemas/samples.schema.yaml) files which are used as input.
[](https://github.com/hydra-genetics/tools/actions/workflows/main.yaml)
[](https://github.com/hydra-genetics/hydra-genetics/actions/workflows/test-build-mkdocs.yaml)
## Functions
* create
* reference
Example of how to generate a new project
```
virtualenv -p python3.9 venv
source venv/bin/activate
pip install hydra-genetics
hydra-genetics create-module -n snv -d "Collection of callers" -a "Patrik S" -e "p.s@mail.se" -g patrik -o snv
# Create new smk file named "samtools.smk" with rule "samtools_rule2"
hydra-genetics create-rule -c rule2 -t samtools -m snv -a test2 -e "test@test"
# Add command to "samtools smk" file, rule name will be "samtools_rule3"
hydra-genetics create-rule -c rule3 -t samtools -m snv -a test2 -e "test@test"
# -t/--tool can be skipped for a single command tool, ex a script
# this will create a smk file named "super_script.smk" with a rule "super_script"
hydra-genetics create-rule -c rule3 -t samtools -m snv -a test2 -e "test@test"
# Create input files
hydra-genetics create-input-files -d path/dir1 -d path/dir2
# Create singularity cache
# all container specified in config.yaml will be fetched
hydra-genetics singularity create-singularity-files -o singularity_cache -c config.yaml
```
Raw data
{
"_id": null,
"home_page": "https://github.com/hydra-genetics/tools",
"name": "hydra-genetics",
"maintainer": null,
"docs_url": null,
"requires_python": null,
"maintainer_email": null,
"keywords": "hydra-genetics, snakemake, bioinformatics, workflow, pipeline, clinical, biology, sequencing, NGS, next generation sequencing",
"author": "Patrik Smeds",
"author_email": "patrik.smeds@scilifelab.uu.se",
"download_url": "https://files.pythonhosted.org/packages/2e/b3/3130323f4eee75ed2d79181f630d378d8f93f8456a712baf9a970ec4260e/hydra_genetics-2.0.1.tar.gz",
"platform": null,
"description": "<p align=\"center\">\n<a href=\"https://hydra-genetics.readthedocs.io\">https://hydra-genetics.readthedocs.io</a>\n</p>\n\n# <img src=\"images/hydragenetics.png\" width=40 /> Hydra-genetics\n\nCommand line interface to create new modules/pipelines or adding a new rule to an existing project. Provides libraries used to make it easier for people not used to pandas to extract information from samples and units dataframes. These dataframes are generated from [units.tsv](https://github.com/hydra-genetics/tools/blob/develop/hydra_genetics/pipeline-template/workflow/schemas/units.schema.yaml) and [samples.tsv](https://github.com/hydra-genetics/prealignment/blob/develop/workflow/schemas/samples.schema.yaml) files which are used as input.\n\n[](https://github.com/hydra-genetics/tools/actions/workflows/main.yaml)\n\n[](https://github.com/hydra-genetics/hydra-genetics/actions/workflows/test-build-mkdocs.yaml)\n\n\n\n## Functions\n\n* create\n* reference\n\n\nExample of how to generate a new project\n```\n virtualenv -p python3.9 venv\n source venv/bin/activate\n pip install hydra-genetics\n hydra-genetics create-module -n snv -d \"Collection of callers\" -a \"Patrik S\" -e \"p.s@mail.se\" -g patrik -o snv\n # Create new smk file named \"samtools.smk\" with rule \"samtools_rule2\"\n hydra-genetics create-rule -c rule2 -t samtools -m snv -a test2 -e \"test@test\"\n # Add command to \"samtools smk\" file, rule name will be \"samtools_rule3\"\n hydra-genetics create-rule -c rule3 -t samtools -m snv -a test2 -e \"test@test\"\n\n # -t/--tool can be skipped for a single command tool, ex a script\n # this will create a smk file named \"super_script.smk\" with a rule \"super_script\"\n hydra-genetics create-rule -c rule3 -t samtools -m snv -a test2 -e \"test@test\"\n\n # Create input files\n hydra-genetics create-input-files -d path/dir1 -d path/dir2\n\n # Create singularity cache\n # all container specified in config.yaml will be fetched\n hydra-genetics singularity create-singularity-files -o singularity_cache -c config.yaml\n\n```\n",
"bugtrack_url": null,
"license": "GPL-3",
"summary": "Helper tools for use with hydra-genetics pipelines.",
"version": "2.0.1",
"project_urls": {
"Homepage": "https://github.com/hydra-genetics/tools"
},
"split_keywords": [
"hydra-genetics",
" snakemake",
" bioinformatics",
" workflow",
" pipeline",
" clinical",
" biology",
" sequencing",
" ngs",
" next generation sequencing"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "2eb33130323f4eee75ed2d79181f630d378d8f93f8456a712baf9a970ec4260e",
"md5": "2900202a060934e20cc8206951b44c64",
"sha256": "4b41c643231d5e6bca878706b9a8949a4b9ba6af4889d32c4db492e7ecf09d32"
},
"downloads": -1,
"filename": "hydra_genetics-2.0.1.tar.gz",
"has_sig": false,
"md5_digest": "2900202a060934e20cc8206951b44c64",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 172815,
"upload_time": "2024-04-25T12:35:31",
"upload_time_iso_8601": "2024-04-25T12:35:31.291005Z",
"url": "https://files.pythonhosted.org/packages/2e/b3/3130323f4eee75ed2d79181f630d378d8f93f8456a712baf9a970ec4260e/hydra_genetics-2.0.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-04-25 12:35:31",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "hydra-genetics",
"github_project": "tools",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "hydra-genetics"
}
JSON
