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taimontgomery merged 4 commits into from
Nov 30, 2022
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Project: tiny-count standalone installation option via bioconda #257

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The tiny-count conda recipe has been accepted by bioconda. Updating R…
AlexTate Nov 30, 2022
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Minor correction in description of GFF file requirements
AlexTate Nov 30, 2022
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Table of contents correction for the installation section link
AlexTate Nov 30, 2022
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Update README.md
taimontgomery Nov 30, 2022
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51 changes: 26 additions & 25 deletions README.md
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Expand Up @@ -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)
Expand All @@ -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
Expand Down Expand Up @@ -90,11 +91,11 @@ tiny get-template

### Requirements for User-Provided Input Files

| Input Type | File Extension | Requirements |
|----------------------------------------------------------------------------|-------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Reference annotations<br/>[(example)](START_HERE/reference_data/ram1.gff3) | GFF3 / GFF2 / GTF | Column 9 attributes (defined as "tag=value" or "tag "):<ul><li>Each feature must have an `ID` or `gene_id` or `Parent` tag (referred to as `ID` henceforth).</li><li>Discontinuous features must be defined with the `Parent` tag whose value is the logical parent's `ID`, or by sharing the same `ID`.</li><li>Attribute values containing commas must represent lists.</li><li>`Parent` tags with multiple values are not yet supported.</li><li>See the example link (left) for col. 9 formatting.</li></ul> |
| Sequencing data<br/>[(example)](START_HERE/fastq_files) | FASTQ(.gz) | Files must be demultiplexed. |
| Reference genome<br/>[(example)](START_HERE/reference_data/ram1.fa) | FASTA | Chromosome identifiers (e.g. Chr1): <ul><li>Should match your reference annotation file chromosome identifiers</li><li>Are case sensitive</li></ul> |
| Input Type | File Extension | Requirements |
|----------------------------------------------------------------------------|-------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Reference annotations<br/>[(example)](START_HERE/reference_data/ram1.gff3) | GFF3 / GFF2 / GTF | Column 9 attributes (defined as "tag=value" or "tag value"):<ul><li>Each feature must have an `ID` or `gene_id` or `Parent` tag (referred to as `ID` henceforth).</li><li>Discontinuous features must be defined with the `Parent` tag whose value is the logical parent's `ID`, or by sharing the same `ID`.</li><li>Attribute values containing commas must represent lists.</li><li>`Parent` tags with multiple values are not yet supported.</li><li>See the example link (left) for col. 9 formatting.</li></ul> |
| Sequencing data<br/>[(example)](START_HERE/fastq_files) | FASTQ(.gz) | Files must be demultiplexed. |
| Reference genome<br/>[(example)](START_HERE/reference_data/ram1.fa) | FASTA | Chromosome identifiers (e.g. Chr1): <ul><li>Should match your reference annotation file chromosome identifiers</li><li>Are case sensitive</li></ul> |



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