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zarp-cli

A user-friendly command-line interface for the ZARP RNA-seq analysis workflow

https://github.com/zavolanlab/zarp-cli

Science Score: 65.0%

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    Found .zenodo.json file
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    Found 4 DOI reference(s) in README
  • ○
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  • ✓
    Institutional organization owner
    Organization zavolanlab has institutional domain (www.biozentrum.unibas.ch)
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    Low similarity (15.5%) to scientific vocabulary

Keywords

bioinformatics cli command-line-interface fair high-throughput library pipeline python reproducible-research rna-seq sequencing snakemake transcriptomics workflow
Last synced: 4 months ago · JSON representation ·

Repository

A user-friendly command-line interface for the ZARP RNA-seq analysis workflow

Basic Info
Statistics
  • Stars: 5
  • Watchers: 4
  • Forks: 1
  • Open Issues: 10
  • Releases: 1
Topics
bioinformatics cli command-line-interface fair high-throughput library pipeline python reproducible-research rna-seq sequencing snakemake transcriptomics workflow
Created almost 5 years ago · Last pushed 4 months ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md

ZARP-cli

License Build_status Docs Coverage GitHub_tag
DOI:zenodo DOI:f1000

: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 package to infer missing metadata and then runs the ZARP RNA-Seq analysis pipeline 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 sample1.fq.gz /path/to/sample2.fq.gz # ZARP two single-end libraries zarp mysample@abcdefgh.fq.gz # assign a sample name zarp mate1.fq.gz,mate2.fq.gz # ZARP one paired-end library zarp table:table.tsv # ZARP all samples from a sample table zarp SRR0123456789 myothersample@SRR0123456789 # ZARP SRA runs zarp \ sample1.fq.gz /path/to/sample2.fq.gz \ mysample@adcdefgh.fg.gz \ mate1.fq.gz,mate2.fq.gz \ table:table.tsv \ SRR0123456789 myothersample@SRR0123456789 # ZARP everything at once! ```

Quick installation

Quick installation requires the following:

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 https://zavolanlab.github.io/zarp-cli.

Versioning

The project adopts the Semantic Versioning 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 if you are interested to contribute. Please mind the code of conduct for all interactions with the community.

Contact

For questions or suggestions regarding the code, please use the issue tracker. For any other inquiries, please contact us by email.

© 2021 Zavolab, Biozentrum, University of Basel

Owner

  • Name: Zavolan Lab
  • Login: zavolanlab
  • Kind: organization
  • Location: Basel

Citation (CITATION.cff) 

# This CITATION.cff file was formatted with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: ZARP-cli
message: >-
  Please cite this software using the metadata from
  'preferred-citation'.
type: software
authors:
  - affiliation: 'Biozentrum, University of Basel'
    family-names: Kanitz
    given-names: Alexander
    orcid: 'https://orcid.org/0000-0002-3468-0652'
  - affiliation: 'Biozentrum, University of Basel'
    family-names: Herrmann
    given-names: Christina J.
    orcid: 'https://orcid.org/0000-0003-1649-3463'
  - affiliation: 'Biozentrum, University of Basel'
    family-names: Bąk
    given-names: Maciej
    orcid: 'https://orcid.org/0000-0003-1361-7301'
  - affiliation: 'Biozentrum, University of Basel'
    family-names: Katsantoni
    given-names: Maria
    orcid: 'https://orcid.org/0000-0003-1961-0223'
  - affiliation: 'Biozentrum, University of Basel'
    family-names: Burri
    given-names: Dominik
    orcid: 'https://orcid.org/0000-0002-8131-9309'
  - affiliation: 'Biozentrum, University of Basel'
    family-names: Balajti
    given-names: Máté
    orcid: 'https://orcid.org/0009-0000-3932-3964'
  - affiliation: 'Biozentrum, University of Basel'
    family-names: Zavolan
    given-names: Mihaela
    orcid: 'https://orcid.org/0000-0002-8832-2041'
identifiers:
  - type: doi
    value: 10.5281/zenodo.10789818
    description: >-
      Collection of archived snapshots of all versions of
      ZARP-cli
  - type: doi
    value: 10.5281/zenodo.10789819
    description: >-
      Archived snapshot of version v1.0.0-rc.1 of My
      Research Software
repository-code: 'https://github.com/zavolanlab/zarp-cli'
url: 'https://zavolanlab.github.io/zarp-cli/'
abstract: >-
  A user-friendly command-line interface for the ZARP
  RNA-seq analysis workflow.
keywords:
  - bioinformatics
  - cli
  - command-line-interface
  - fair
  - high-throughput
  - library
  - pipeline
  - python
  - reproducible-research
  - rna-seq
  - sequencing
  - transcriptomics
  - workflow
license: Apache-2.0
commit: 4f861767029905ae543d7eb6d9772cae457e3f00
version: v1.0.0-rc.1
date-released: '2024-03-06'
contact:
  - address: Spitalstrasse 41
    city: Basel
    country: CH
    email: zavolab-biozentrum@unibas.ch
    location: 'Biozentrum, room 08.004'
    name: 'Zavolab, Biozentrum, University of Basel'
    post-code: 4056
    region: Basel-Stadt
    website: >-
      https://www.biozentrum.unibas.ch/research/research-groups/research-groups-a-z/overview/unit/research-group-mihaela-zavolan
  - affiliation: 'Biozentrum, University of Basel'
    email: alexander.kanitz@alumni.ethz.ch
    family-names: Kanitz
    given-names: Alexander
    orcid: 'https://orcid.org/0000-0002-3468-0652'
preferred-citation:
  abstract: >-
    BACKGROUND: RNA sequencing (RNA-seq) is a widely used technique in many
    scientific studies. Given the plethora of models and software packages that
    have been developed for processing and analyzing RNA-seq datasets, choosing
    the most appropriate ones is a time-consuming process that requires an
    in-depth understanding of the data, as well as of the principles and
    parameters of each tool. In addition, packages designed for individual tasks
    are developed in different programming languages and have dependencies of
    various degrees of complexity, which renders their installation and
    execution challenging for users with limited computational expertise.
    Workflow languages and execution engines with support for virtualization and
    encapsulation options such as containers and Conda environments facilitate
    these tasks considerably. The resulting computational workflows can then be
    reliably shared with the scientific community, enhancing reusability and the
    reproducibility of results as individual analysis steps are becoming more
    transparent and portable. METHODS: Here we present ZARP, a general purpose
    RNA-seq analysis workflow that builds on state-of-the-art software in the
    field to facilitate the analysis of RNA-seq datasets. ZARP is developed in
    the Snakemake workflow language and can run locally or in a cluster
    environment, generating extensive reports not only of the data but also of
    the options utilized. It is built using modern technologies with the
    ultimate goal to reduce the hands-on time for bioinformaticians and
    non-expert users and serve as a template for future workflow development. To
    this end, we also provide ZARP-cli, a dedicated command-line interface that
    may make running ZARP on an RNA-seq library of interest as easy as executing
    a single two-word command. CONCLUSIONS: ZARP is a powerful RNA-seq analysis
    workflow that is easy to use even for beginners, built using best software
    development practices, available under a permissive Open Source license and
    open to contributions by the scientific community.
  authors:
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Katsantoni
      given-names: Maria
      orcid: 'https://orcid.org/0000-0003-1961-0223'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Gypas
      given-names: Foivos
      orcid: 'https://orcid.org/0000-0002-7233-8794'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Herrmann
      given-names: Christina J.
      orcid: 'https://orcid.org/0000-0003-1649-3463'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Burri
      given-names: Dominik
      orcid: 'https://orcid.org/0000-0002-8131-9309'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Bąk
      given-names: Maciej
      orcid: 'https://orcid.org/0000-0003-1361-7301'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Iborra
      given-names: Paula
      orcid: 'https://orcid.org/0000-0003-0504-3029'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Agarwal
      given-names: Krish
      orcid: 'https://orcid.org/0000-0001-6809-5024'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Ataman
      given-names: Meriç
      orcid: 'https://orcid.org/0000-0002-7942-9226'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Balajti
      given-names: Máté
      orcid: 'https://orcid.org/0009-0000-3932-3964'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Pozzan
      given-names: Noè
      orcid: 'https://orcid.org/0009-0007-0466-8269'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Schlusser
      given-names: Niels
      orcid: 'https://orcid.org/0000-0002-3534-2153'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Moon
      given-names: Youngbin
      orcid: 'https://orcid.org/0009-0001-5728-3959'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Mironov
      given-names: Aleksei
      orcid: 'https://orcid.org/0000-0003-4228-7022'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Börsch
      given-names: Anastasiya
      orcid: 'https://orcid.org/0000-0003-3392-5272'
    - affiliation: 'Biozentrum, University of Basel'
      family-names: Zavolan
      given-names: Mihaela
      orcid: 'https://orcid.org/0000-0002-8832-2041'
    - affiliation: 'Biozentrum, University of Basel'
      country: CH
      family-names: Kanitz
      given-names: Alexander
      orcid: 'https://orcid.org/0000-0002-3468-0652'
  contact:
    - address: Spitalstrasse 41
      city: Basel
      country: CH
      email: zavolab-biozentrum@unibas.ch
      location: 'Biozentrum, room 08.004'
      name: 'Zavolab, Biozentrum, University of Basel'
      post-code: 4056
      region: Basel-Stadt
      website: >-
        https://www.biozentrum.unibas.ch/research/research-groups/research-groups-a-z/overview/unit/research-group-mihaela-zavolan
    - affiliation: 'Biozentrum, University of Basel'
      email: alexander.kanitz@unibas.ch
      family-names: Kanitz
      given-names: Alexander
      orcid: 'https://orcid.org/0000-0002-3468-0652'
    - affiliation: 'Biozentrum, University of Basel'
      email: mihaela.zavolan@unibas.ch
      family-names: Zavolan
      given-names: Mihaela
      orcid: 'https://orcid.org/0000-0002-8832-2041'
  copyright: © 2024 Katsantoni M et al.
  date-published: '2024-05-24'
  department: Biozentrum
  doi: 10.12688/f1000research.149237.1
  institution:
    name: University of Basel
  issn: 2046-1402
  journal: F1000Research
  keywords:
    - bioinformatics
    - computational workflow
    - data analysis
    - high-throughput
    - reproducibility
    - RNA-seq
    - transcriptomics
    - usability
  languages:
    - en
  license: CC-BY-4.0
  month: 5
  notes: Article describing the ZARP workflow and its command-line interface ZARP-cli.
  number: 533
  publisher:
    name: F1000 Research Ltd
  status: preprint
  title: 'ZARP: A user-friendly and versatile RNA-seq analysis workflow'
  type: article
  url: 'https://f1000research.com/articles/13-533/v1'
  version: 1
  volume: 13
  year: 2024
references:
  - authors:
      - name: genomepy team
    doi: 10.5281/zenodo.1010458
    license: MIT
    repository-code: 'https://github.com/vanheeringen-lab/genomepy'
    title: genomepy
    type: software
    url: 'https://vanheeringen-lab.github.io/genomepy/'
  - authors:
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Kanitz
        given-names: Alexander
        orcid: 'https://orcid.org/0000-0002-3468-0652'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Balajti
        given-names: Máté
        orcid: 'https://orcid.org/0009-0000-3932-3964'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Kandari
        given-names: Rohan
      - affiliation: 'Institute of Computer Science, Masaryk University'
        family-names: Jurič
        given-names: Boris
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Herrmann
        given-names: Christina J.
        orcid: 'https://orcid.org/0000-0003-1649-3463'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: How
        given-names: Hiap Chon
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Bąk
        given-names: Maciej
        orcid: 'https://orcid.org/0000-0003-1361-7301'
    license: Apache-2.0
    repository-code: 'https://github.com/zavolanlab/htsinfer'
    title: HTSinfer
    type: software
  - authors:
      - name: Snakemake team
    license: MIT
    repository-code: 'https://github.com/snakemake/snakemake'
    title: Snakemake
    type: software
    url: 'https://snakemake.github.io/'
  - authors:
      - name: SRA Tools team
    license-url: >-
      https://github.com/ncbi/sra-tools/blob/0cf634c2fb641cd55c6bff987c95ac669273eea9/LICENSE
    repository-code: 'https://github.com/ncbi/sra-tools'
    title: SRA Tools
    type: software
  - authors:
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Katsantoni
        given-names: Maria
        orcid: 'https://orcid.org/0000-0003-1961-0223'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Kanitz
        given-names: Alexander
        orcid: 'https://orcid.org/0000-0002-3468-0652'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Herrmann
        given-names: Christina J.
        orcid: 'https://orcid.org/0000-0003-1649-3463'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Burri
        given-names: Dominik
        orcid: 'https://orcid.org/0000-0002-8131-9309'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Gypas
        given-names: Foivos
        orcid: 'https://orcid.org/0000-0002-7233-8794'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Bąk
        given-names: Maciej
        orcid: 'https://orcid.org/0000-0003-1361-7301'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Balajti
        given-names: Máté
        orcid: 'https://orcid.org/0009-0000-3932-3964'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Pozzan
        given-names: Noè
        orcid: 'https://orcid.org/0009-0007-0466-8269'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Ataman
        given-names: Meriç
        orcid: 'https://orcid.org/0000-0002-7942-9226'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Zavolan
        given-names: Mihaela
        orcid: 'https://orcid.org/0000-0002-8832-2041'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Schlusser
        given-names: Niels
        orcid: 'https://orcid.org/0000-0002-3534-2153'
      - affiliation: 'Biozentrum, University of Basel'
        family-names: Mironov
        given-names: Aleksei
        orcid: 'https://orcid.org/0000-0003-4228-7022'
    license: Apache-2.0
    repository-code: 'https://github.com/zavolanlab/htsinfer'
    title: ZARP
    type: software
    url: 'https://zavolanlab.github.io/zarp/'

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Dependencies

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