From 5c8fe021795d577fb570e589301de6fcd2f15f8e Mon Sep 17 00:00:00 2001 From: farchaab Date: Fri, 20 Dec 2024 12:14:43 +0100 Subject: [PATCH 1/2] update readme --- README.md | 27 ++++++++++++++++----------- 1 file changed, 16 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 56f8b6b..d44d5e2 100644 --- a/README.md +++ b/README.md @@ -1,41 +1,46 @@ # assembly_finder [![tests](https://github.com/metagenlab/assembly_finder/actions/workflows/unit-tests.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/unit-tests.yml) [![docs](https://github.com/metagenlab/assembly_finder/actions/workflows/build-docs.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/build-docs.yml) -[![docs](https://github.com/metagenlab/assembly_finder/actions/workflows/docker-publish.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/docker-publish.yml) +[![docker](https://github.com/metagenlab/assembly_finder/actions/workflows/docker-publish.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/docker-publish.yml) -[![](https://img.shields.io/static/v1?label=CLI&message=Snaketool&color=blueviolet)](https://github.com/beardymcjohnface/Snaketool) +[![snaketool](https://img.shields.io/static/v1?label=CLI&message=Snaketool&color=blueviolet)](https://github.com/beardymcjohnface/Snaketool) [![license](https://img.shields.io/github/license/metagenlab/assembly_finder.svg)](https://github.com/metagenlab/assembly_finder/blob/main/LICENSE) [![version](https://img.shields.io/conda/vn/bioconda/assembly_finder)](http://bioconda.github.io/recipes/assembly_finder/README.html) [![downloads](https://img.shields.io/conda/dn/bioconda/assembly_finder)](https://anaconda.org/bioconda/assembly_finder) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13353494.svg)](https://zenodo.org/doi/10.5281/zenodo.13353494) -assembly_finder is a [Snakemake](https://github.com/snakemake/snakemake)-powered cli to download genomes with [NCBI datasets](https://github.com/ncbi/datasets). +`assembly_finder` is a [Snakemake](https://github.com/snakemake/snakemake)-powered cli, written in [Snaketool](https://github.com/beardymcjohnface/Snaketool), to download genomes with [NCBI datasets](https://github.com/ncbi/datasets). ## :zap: Quick start ### Installation -#### Mamba +#### [Conda](https://github.com/conda-forge/miniforge) ```sh -mamba create -n assembly_finder assembly_finder +conda create -n assembly_finder assembly_finder ``` -#### Docker + +> [!NOTE] +> Miniforge is the recommended conda-based distribution + + +#### [Apptainer](https://github.com/apptainer/apptainer) ```sh -docker pull ghcr.io/metagenlab/assembly_finder:latest +apptainer pull docker://ghcr.io/metagenlab/assembly_finder:latest ``` ### Usage -#### Mamba +#### Conda ```sh assembly_finder -i staphylococcus_aureus -nb 1 ``` -#### Docker +#### Apptainer ```sh -docker run ghcr.io/metagenlab/assembly_finder:latest \ +apptainer run docker://ghcr.io/metagenlab/assembly_finder:latest \ assembly_finder -i staphylococcus_aureus -nb 1 --no-use-conda ``` > [!NOTE] -> set --no-use-conda when running via docker +> set --no-use-conda when running in a container ### Output From d2d69cd2ad1f31fc24f8800e9a6bda7d3830ffcc Mon Sep 17 00:00:00 2001 From: farchaab Date: Fri, 20 Dec 2024 12:14:51 +0100 Subject: [PATCH 2/2] update docs --- docs/examples.md | 2 +- docs/index.md | 17 +++++++++-------- docs/inputs.md | 6 +++--- 3 files changed, 13 insertions(+), 12 deletions(-) diff --git a/docs/examples.md b/docs/examples.md index f00e8f6..8a76ec5 100644 --- a/docs/examples.md +++ b/docs/examples.md @@ -1,6 +1,6 @@ ## Download tables -Starting from version `0.8.0`, you can restrict outputs to `assembly_summary.tsv` and `taxonomy.tsv` +Starting from [v0.8.0](https://github.com/metagenlab/assembly_finder/releases/tag/v0.8.0), you can restrict outputs to `assembly_summary.tsv` and `taxonomy.tsv` * Command diff --git a/docs/index.md b/docs/index.md index f45605d..156840d 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,30 +1,31 @@ # assembly_finder [![tests](https://github.com/metagenlab/assembly_finder/actions/workflows/unit-tests.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/unit-tests.yml) [![docs](https://github.com/metagenlab/assembly_finder/actions/workflows/build-docs.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/build-docs.yml) -[![docs](https://github.com/metagenlab/assembly_finder/actions/workflows/docker-publish.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/docker-publish.yml) +[![docker](https://github.com/metagenlab/assembly_finder/actions/workflows/docker-publish.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/docker-publish.yml) -[![](https://img.shields.io/static/v1?label=CLI&message=Snaketool&color=blueviolet)](https://github.com/beardymcjohnface/Snaketool) +[![snaketool](https://img.shields.io/static/v1?label=CLI&message=Snaketool&color=blueviolet)](https://github.com/beardymcjohnface/Snaketool) [![license](https://img.shields.io/github/license/metagenlab/assembly_finder.svg)](https://github.com/metagenlab/assembly_finder/blob/main/LICENSE) [![version](https://img.shields.io/conda/vn/bioconda/assembly_finder)](http://bioconda.github.io/recipes/assembly_finder/README.html) [![downloads](https://img.shields.io/conda/dn/bioconda/assembly_finder)](https://anaconda.org/bioconda/assembly_finder) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13353494.svg)](https://zenodo.org/doi/10.5281/zenodo.13353494) -assembly_finder is a [Snakemake](https://github.com/snakemake/snakemake)-powered cli to download genomes with [NCBI datasets](https://github.com/ncbi/datasets). +`assembly_finder` is a [Snakemake](https://github.com/snakemake/snakemake)-powered cli, written in [Snaketool](https://github.com/beardymcjohnface/Snaketool), to download genomes with [NCBI datasets](https://github.com/ncbi/datasets). ## Installation -=== "mamba (recommended)" +=== "Conda (recommended)" ```sh - mamba create -n assembly_finder assembly_finder + conda create -n assembly_finder assembly_finder ``` !!! note Requires a [Miniforge](https://github.com/conda-forge/miniforge) installation -=== "docker" + +=== "Apptainer" ```sh - docker pull ghcr.io/metagenlab/assembly_finder:latest + apptainer pull docker://ghcr.io/metagenlab/assembly_finder:latest ``` !!! note @@ -51,7 +52,7 @@ assembly_finder is a [Snakemake](https://github.com/snakemake/snakemake)-powered === "container" ```sh - docker run ghcr.io/metagenlab/assembly_finder:latest \ + apptainer run docker://ghcr.io/metagenlab/assembly_finder:latest \ assembly_finder -i staphylococcus_aureus -nb 1 --no-use-conda ``` diff --git a/docs/inputs.md b/docs/inputs.md index 324da2d..1216a32 100644 --- a/docs/inputs.md +++ b/docs/inputs.md @@ -1,6 +1,6 @@ # Inputs -Input can be either a string or a table, and queries can be either taxa or accession as shown in [NCBI datasets docs](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install). +Input can be either a string or a table, and queries can be either taxa or accessions as shown in [NCBI datasets docs](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install). ## Strings @@ -17,8 +17,8 @@ Input can be either a string or a table, and queries can be either taxa or acces === "Accessions" ```sh - assembly_finder --accession -i GCF_003812505.1,\ - GCF_000418345.1,GCF_000157115.2 -o accessions + assembly_finder --accession -i GCF_003812505.1,GCF_000418345.1,GCF_000157115.2 \ + -o accessions ``` !!! note