diff --git a/README.md b/README.md index 7c177b95..7a1f3889 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ *Feedback, suggestions, and bug reports are welcome under the [issues tab](https://github.com/MontgomeryLab/tinyrna/issues). Thank you!* -- [Installation](#installation) +- [Installation](#tinyrna-installation) - [Usage](#usage) - [Configuration Files](#configuration-files) - [User-Provided Input Files](#requirements-for-user-provided-input-files) @@ -26,39 +26,40 @@ tinyRNA is a set of tools to simplify the analysis of next-generation sequencing ![tinyRNA basic pipeline](images/tinyrna-workflow_current.png) -## Installation +## tinyRNA Installation -A setup script has been provided for easy installation of tinyRNA. First, download the latest release of tinyRNA from the [Releases link](https://github.com/MontgomeryLab/tinyRNA/releases) on the right sidebar. Decompress the downloaded file and navigate to the resulting directory in your terminal, then execute the setup script: +### Stable Releases +1. Download the latest release from the [releases link](https://github.com/MontgomeryLab/tinyRNA/releases) on the sidebar +2. Decompress the archive and navigate to the resulting directory in your terminal +3. Run `./setup.sh` to install the project and its dependencies in a conda environment named "tinyrna" +#### Installation Tips +- If the installation script runs the Miniconda installer: + - Press "q" if you find yourself trapped on the license page + - We recommend answering "yes" to running `conda init` +- A custom environment name can be passed as the first argument to `setup.sh` + +### Development Releases +This option provides the latest features but stable releases are more rigorously tested. ```shell -# Change into the tinyRNA directory (include path relative to your working directory) - cd tinyRNA-1.2.0 +# Clone the repository into a local directory + git clone https://github.com/MontgomeryLab/tinyrna.git + cd tinyrna # Install the tinyrna environment and dependencies ./setup.sh - -# This will install the project and its dependencies in a conda environment named `tinyrna`. ``` -If the installation script runs the Miniconda installer: -- Press "q" if you find yourself trapped on the license page -- We recommend answering "yes" to running `conda init` - -Alternatively, to install the latest development of tinyRNA, which is not subject to as rigorous of testing but may contain features lacking in the latest release, within your terminal clone the repository using git: +## tiny-count installation +Alternatively, you can install tinyRNA's precision counting tool by itself. Unlike the full tinyRNA suite, this option can be installed in existing conda environments and requires fewer dependencies. ```shell -# Clone the repository into a local directory and change into the tinyRNA directory - git clone https://github.com/MontgomeryLab/tinyrna.git - cd tinyrna - -# Install the tinyrna environment and dependencies -# A custom environment name can also be passed as a command line argument - ./setup.sh +conda install -c bioconda -c conda-forge tiny-count ``` ## Usage -The `tinyrna` conda environment must be activated before use. +The `tinyrna` conda environment must be activated before using the tinyRNA workflow. ```shell # Activate the tinyrna environment conda activate tinyrna @@ -90,11 +91,11 @@ tiny get-template ### Requirements for User-Provided Input Files -| Input Type | File Extension | Requirements | -|----------------------------------------------------------------------------|-------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| Reference annotations
[(example)](START_HERE/reference_data/ram1.gff3) | GFF3 / GFF2 / GTF | Column 9 attributes (defined as "tag=value" or "tag "): | -| Sequencing data
[(example)](START_HERE/fastq_files) | FASTQ(.gz) | Files must be demultiplexed. | -| Reference genome
[(example)](START_HERE/reference_data/ram1.fa) | FASTA | Chromosome identifiers (e.g. Chr1): | +| Input Type | File Extension | Requirements | +|----------------------------------------------------------------------------|-------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| Reference annotations
[(example)](START_HERE/reference_data/ram1.gff3) | GFF3 / GFF2 / GTF | Column 9 attributes (defined as "tag=value" or "tag value"): | +| Sequencing data
[(example)](START_HERE/fastq_files) | FASTQ(.gz) | Files must be demultiplexed. | +| Reference genome
[(example)](START_HERE/reference_data/ram1.fa) | FASTA | Chromosome identifiers (e.g. Chr1): |