fgsmk
A set of utility functions for use in Snakemake workflows. Supports Snakemake 8+.
Table of Contents
Recommended Installation
This package is intended for use within a Snakemake workflow project.
Install the Python package and dependency management tool poetry using official documentation.
You must have Python 3.11 or greater available on your system path, which could be managed by mamba, pyenv, or another package manager.
If you have a mamba environment for the parent project, activate it first.
Install with poetry.
poetry install
Usage
Error summary file
Set the onerror directive in a Snakemake workflow to point to the fgsmk.on_error function.
from fgsmk.log import on_error
onerror:
on_error(snakefile=Path(__file__), config=config, log=Path(log))
"""Block of code that gets called if the snakemake pipeline exits with an error."""
This will produce a file error_summary.txt containing the last (up to) 50 lines of the log files of any rules that failed execution.
The content will also be output to stdout.
Development and Testing
See the contributing guide for more information.
1 maintainer
Metadata
1 maintainer
Release files for fgsmk 1.0.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| fgsmk-1.0.0.tar.gz | 10.4 kB | With provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| fgsmk-1.0.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 19.6 kB
Release files / fgsmk-1.0.0.tar.gz
| Download URL | fgsmk-1.0.0.tar.gz |
|---|---|
| Size | 10.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Transparency logRelease files / fgsmk-1.0.0-py3-none-any.whl
| Download URL | fgsmk-1.0.0-py3-none-any.whl |
|---|---|
| Size | 9.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
0ccf67752bdc6fbd4a72df1a5db01b61242761978dd68d071c719be5aeb861b0
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BLAKE2b-256 checksum How to use checksums |
4b193a0f7cb4744c0cdceeaf503ca83c0e1cda93541358b061124c81eb206bb2
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 17, 2026.
Transparency logSecurity for fgsmk 1.0.0
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
Full provenance
All 2 files in this release have been uploaded with provenance metadata.
Attestation for fgsmk-1.0.0.tar.gz
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 17, 2026.
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