From 8eddcca239d9c1040a9a931021d19122b7b87019 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 30 Nov 2022 08:13:50 -0800
Subject: [PATCH 1/4] The tiny-count conda recipe has been accepted by
bioconda. Updating README.md to include this installation option
---
README.md | 37 +++++++++++++++++++------------------
1 file changed, 19 insertions(+), 18 deletions(-)
diff --git a/README.md b/README.md
index 7c177b95..cc8f6d46 100644
--- a/README.md
+++ b/README.md
@@ -26,34 +26,35 @@ tinyRNA is a set of tools to simplify the analysis of next-generation sequencing
-## 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
From 62ebe001fafbfdf0e4ab0d00c18431d71eaa64d0 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 30 Nov 2022 08:43:43 -0800
Subject: [PATCH 2/4] Minor correction in description of GFF file requirements
---
README.md | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/README.md b/README.md
index cc8f6d46..836d5371 100644
--- a/README.md
+++ b/README.md
@@ -91,11 +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 "):- Each feature must have an `ID` or `gene_id` or `Parent` tag (referred to as `ID` henceforth).
- Discontinuous features must be defined with the `Parent` tag whose value is the logical parent's `ID`, or by sharing the same `ID`.
- Attribute values containing commas must represent lists.
- `Parent` tags with multiple values are not yet supported.
- See the example link (left) for col. 9 formatting.
|
-| 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): - Should match your reference annotation file chromosome identifiers
- Are case sensitive
|
+| 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"):- Each feature must have an `ID` or `gene_id` or `Parent` tag (referred to as `ID` henceforth).
- Discontinuous features must be defined with the `Parent` tag whose value is the logical parent's `ID`, or by sharing the same `ID`.
- Attribute values containing commas must represent lists.
- `Parent` tags with multiple values are not yet supported.
- See the example link (left) for col. 9 formatting.
|
+| 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): - Should match your reference annotation file chromosome identifiers
- Are case sensitive
|
From c6d9efb79615758fcaca8aef28d79419c482f1d0 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 30 Nov 2022 09:59:26 -0800
Subject: [PATCH 3/4] Table of contents correction for the installation section
link
---
README.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/README.md b/README.md
index 836d5371..ebc87a16 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)
From 5dcb57b8ab5d65480d6e1b8a99995bcf3ae8ad40 Mon Sep 17 00:00:00 2001
From: taimontgomery <35973177+taimontgomery@users.noreply.github.com>
Date: Wed, 30 Nov 2022 13:04:27 -0700
Subject: [PATCH 4/4] Update README.md
---
README.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/README.md b/README.md
index ebc87a16..7a1f3889 100644
--- a/README.md
+++ b/README.md
@@ -59,7 +59,7 @@ 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