From 9aff2b75f8ec7f6fd2fcce7839c95527129d9415 Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Tue, 13 Feb 2024 12:12:04 +0100 Subject: [PATCH] docs: update ZARP-cli installation instructions --- README.md | 66 +++++++++++++++++++------------------ install/environment.cli.yml | 6 ---- 2 files changed, 34 insertions(+), 38 deletions(-) delete mode 100644 install/environment.cli.yml diff --git a/README.md b/README.md index e205948..d2e1e22 100644 --- a/README.md +++ b/README.md @@ -8,24 +8,35 @@ -**ZARP** ([Zavolan-Lab][zavolan-lab] Automated RNA-Seq Pipeline) is a generic RNA-Seq analysis workflow that allows -users to process and analyze Illumina short-read sequencing libraries with minimum effort. The workflow relies on -publicly available bioinformatics tools and currently handles single or paired-end stranded bulk RNA-seq data. -The workflow is developed in [Snakemake][snakemake], a widely used workflow management system in the bioinformatics -community. - -According to the current ZARP implementation, reads are analyzed (pre-processed, aligned, quantified) with state-of-the-art -tools to give meaningful initial insights into the quality and composition of an RNA-Seq library, reducing hands-on time for bioinformaticians and giving experimentalists the possibility to rapidly assess their data. Additional reports summarise the results of the individual steps and provide useful visualisations. +**ZARP** ([Zavolab][zavolan-lab] Automated RNA-seq Pipeline) is a generic +RNA-Seq analysis workflow that allows users to process and analyze Illumina +short-read sequencing libraries with minimum effort. Better yet: With our +companion [**ZARP-cli**](https://github.com/zavolanlab/zarp-cli) command line +interface, you can start ZARP runs with the simplest and most intuitive +commands. + +_RNA-seq analysis doesn't get simpler than that!_ + +ZARP relies on publicly available bioinformatics tools and currently handles +single or paired-end stranded bulk RNA-seq data. The workflow is developed in +[Snakemake][snakemake], a widely used workflow management system in the +bioinformatics community. + +ZARP will pre-process, align and quantify your single- or paired-end stranded +bulk RNA-seq sequencing libraries with publicly available state-of-the-art +bioinformatics tools. ZARP's browser-based rich reports and visualitations will +give you meaningful initial insights in the quality and composition of your +sequencing experiments - fast and simple. Whether you are an experimentalist +struggling with large scale data analysis or an experienced bioinformatician, +when there's RNA-seq data to analyze, just _zarp 'em_!
- > **Note:** For a more detailed description of each step, please refer to the [workflow > documentation][pipeline-documentation]. - # Requirements The workflow has been tested on: @@ -39,6 +50,12 @@ The workflow has been tested on: # Installation +> **IMPORTANT: Rather than installing the ZARP workflow as described in this section, we +> recommend installing [ZARP-cli](https://github.com/zavolanlab/zarp-cli) for most use +> cases!** If you follow its [installation +> instructions](https://zavolanlab.github.io/zarp-cli/guides/installation/), you can +> skip the instructions below. + ## 1. Clone the repository Go to the desired directory/folder on your file system, then clone/get the @@ -105,17 +122,6 @@ to include Singularity in the Conda environment: mamba env update -f install/environment.root.yml ``` -### Command-line interface dependencies -> A command-line interface, [ZARP-cli](https://github.com/zavolanlab/zarp-cli) is now availble and all you have to do to make use of it is update your environment: - -```bash -mamba env update -f install/environment.cli.yml -``` - -More info at: [NEW: Running ZARP gets even easier!](#new-running-zarp-gets-even-easier) - - - ## 4. Activate environment Activate the Conda environment with: @@ -177,22 +183,18 @@ bash tests/test_integration_workflow_with_conda/test.slurm.sh # Running the workflow on your own samples -## NEW: Running ZARP gets even easier! -> You can now run your ZARP workflow using its' new command-line interface, [ZARP-cli](https://github.com/zavolanlab/zarp-cli). To enable ZARP-cli, simply install the additional dependencies by executing the following command _in your active Conda environment_: +## Running ZARP with ZARP-cli (recommended) -```bash -mamba env update -f install/environment.cli.yml -``` -Run: -``` -zarp --help -``` -to see the useful options available, or take a look at [ZARP-cli documentation](https://github.com/zavolanlab/zarp-cli) +Head over to the [ZARP-cli](https://zavolanlab.github.io/zarp-cli/) to learn how to +start ZARP runs with very simple commands, like: +```sh +zarp SRR23590181 +``` ## Running ZARP without ZARP-cli -1. Assuming that your current directory is the repository's root directory, +1. Assuming that your current directory is the workflow repository's root directory, create a directory for your workflow run and move into it with: ```bash diff --git a/install/environment.cli.yml b/install/environment.cli.yml deleted file mode 100644 index 65ff942..0000000 --- a/install/environment.cli.yml +++ /dev/null @@ -1,6 +0,0 @@ -name: zarp -channels: - - conda-forge - - bioconda -dependencies: - - zarp>=0.1