https://hydra-genetics.readthedocs.io
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 and samples.tsv files which are used as input.
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
1 maintainer
Release files for hydra-genetics 4.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| hydra_genetics-4.1.1.tar.gz | 3.3 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| hydra_genetics-4.1.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 3.5 MB
Release files / hydra_genetics-4.1.1.tar.gz
| Download URL | hydra_genetics-4.1.1.tar.gz |
|---|---|
| Size | 3.3 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
42da67f94866abda5347dc4d8a07b1ba79019529e254e758d6d4b8cfe9ce94b5
|
|
BLAKE2b-256 checksum How to use checksums |
ab9c1efd296e429780e24659c2dc27b05635983cfa3fc2c20d46f6043470064f
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.13.12
|
Release files / hydra_genetics-4.1.1-py3-none-any.whl
| Download URL | hydra_genetics-4.1.1-py3-none-any.whl |
|---|---|
| Size | 216.5 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
985fc01bfc1deafb58dbebde8e930f7ad8c7263fcca762847184dad16f799c24
|
|
BLAKE2b-256 checksum How to use checksums |
761d555c1eaa63094127989dc8a414ffeabce438ca3b7aa96486c5ced91bf42b
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.13.12
|
