https://github.com/zavolanlab/zarp-cli
A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
https://github.com/zavolanlab/zarp-cli
bioinformatics cli command-line-interface fair high-throughput library pipeline python reproducible-research rna-seq sequencing snakemake transcriptomics workflow
Last synced: 18 days ago
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A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
- Host: GitHub
- URL: https://github.com/zavolanlab/zarp-cli
- Owner: zavolanlab
- License: apache-2.0
- Created: 2021-02-26T09:01:18.000Z (almost 5 years ago)
- Default Branch: dev
- Last Pushed: 2025-08-26T11:13:20.000Z (5 months ago)
- Last Synced: 2025-10-29T10:42:43.589Z (3 months ago)
- Topics: bioinformatics, cli, command-line-interface, fair, high-throughput, library, pipeline, python, reproducible-research, rna-seq, sequencing, snakemake, transcriptomics, workflow
- Language: Python
- Homepage: https://zavolanlab.github.io/zarp-cli/
- Size: 42.9 MB
- Stars: 5
- Watchers: 4
- Forks: 1
- Open Issues: 10
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff
Awesome Lists containing this project
README
# ZARP-cli
[![License][badge-license]][badge-url-license]
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:pill: **_ZARP_** - RNA-Seq analysis made easy! :syringe:
## Synopsis
- You have a bunch of RNA-Seq samples and wanna know what's in them? **_ZARP
'em!_**
- You have an extensive SRA query with hundreds of runs and you don't know
where to start? **Easy - _ZARP 'em!_**
- Barry left you some samples to analyze and then went on vacation, again? **No
problem, _ZARP 'em!_**
ZARP-cli uses the [HTSinfer][htsinfer] package to infer missing metadata and
then runs the [ZARP RNA-Seq analysis pipeline][zarp] on your samples. Impress
your colleagues with your sudden productivity boost. Or better yet, use the
time saved to go on that camping trip with Barry. Just make sure to guard your
secret! :wink:
## Basic usage
```sh
zarp [-h] [--init] [--verbosity {DEBUG,INFO,WARN,ERROR,CRITICAL}] [--version]
PATH/ID [PATH/ID ...]
# Examples
zarp --init # set up user defaults for ZARP
zarp sample_1.fq.gz /path/to/sample_2.fq.gz # ZARP two single-end libraries
zarp my_sample@abcdefgh.fq.gz # assign a sample name
zarp mate_1.fq.gz,mate_2.fq.gz # ZARP one paired-end library
zarp table:table.tsv # ZARP all samples from a sample table
zarp SRR0123456789 my_other_sample@SRR0123456789 # ZARP SRA runs
zarp \
sample_1.fq.gz /path/to/sample_2.fq.gz \
my_sample@adcdefgh.fg.gz \
mate_1.fq.gz,mate_2.fq.gz \
table:table.tsv \
SRR0123456789 my_other_sample@SRR0123456789 # ZARP everything at once!
```
## Quick installation
Quick installation requires the following:
- Linux with root permissions
- [`conda >= 22.11.1`][conda]
- [`mamba >=1.3.0`][mamba]
Execute the following commands:
```sh
git clone git@github.com:zavolanlab/zarp
git clone git@github.com:zavolanlab/zarp-cli.git
cd zarp-cli
mamba env create -f install/environment.root.yml
conda activate zarp-cli
```
> If you do not have root privileges on your machine, replace the `mamba env
> create` call with the following one:
>
> ```sh
> mamba env create -f install/environment.yml
> ```
That's it - you can now use _ZARP-cli_!
## Documentation
We have designed _ZARP-cli_ to be easy to use. However, there are still a lot
of ways in which execution can be tweaked. For the full documentation visit
****.
## Versioning
The project adopts the [Semantic Versioning][semver] specification for
versioning. Currently the service is still in beta stage, so the API may change
and even break without further notice. However, we are planning to release a
`1.0.0` release as soon as we feel that the software is reasonably stable and
"feature complete" for all of the major use cases we wish to cover.
## Contributing
This project lives off your contributions, be it in the form of bug reports,
feature requests, discussions, or fixes and other code changes. Please refer
to the [contributing guidelines](CONTRIBUTING.md) if you are interested to
contribute. Please mind the [code of conduct](CODE_OF_CONDUCT.md) for all
interactions with the community.
## Contact
For questions or suggestions regarding the code, please use the
[issue tracker][issue-tracker]. For any other inquiries, please contact us
by [email][contact].
© 2021 [Zavolab, Biozentrum, University of Basel][zavolab]
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