Skip to content

v0.1-r1 descriptions, add lastest update section #8

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
aquaskyline merged 1 commit into from
May 18, 2021
Merged

v0.1-r1 descriptions, add lastest update section #8

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
72 changes: 41 additions & 31 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,15 +22,27 @@ Clair3 is the 3<sup>rd</sup> generation of [Clair](https://github.com/HKU-BAL/Cl

---

## Lastest Updates

We are actively fixing bugs and issues in Clair3 reported by users.

*v0.1-r1 (May 18)* : 1. Support relative path ([#5](https://github.com/HKU-BAL/Clair3/issues/5)). 2. Fix `taskset` CPU-core visibility and provide a Singularity image [#6](https://github.com/HKU-BAL/Clair3/issues/6).

*v0.1 (May 17)*: Initial release.

---

## Contents

* [Introduction](#introduction)
* [Latest Updates](#latest-updates)
* [What's New in Clair3](#whats-new-in-clair3)
* [Installation](#installation)
+ [Option 1. Docker pre-built image (recommended)](#option-1--docker-pre-built-image-recommended)
+ [Option 2. Docker Dockerfile](#option-2-docker-dockerfile)
+ [Option 3. Build an anaconda virtual environment](#option-3-build-an-anaconda-virtual-environment)
+ [Option 4. Singularity](#option-4-singularity)
+ [Option 1. Docker pre-built image](#option-1--docker-pre-built-image)
+ [Option 2. Singularity](#option-2--singularity)
+ [Option 3. Docker Dockerfile](#option-3-docker-dockerfile)
+ [Option 4. Build an anaconda virtual environment](#option-4-build-an-anaconda-virtual-environment)
+
* [Quick Demo](#quick-demo)
* [Usage](#usage)
* [Folder Structure and Submodule Descriptions](#folder-structure-and-submodule-descriptions)
Expand Down Expand Up @@ -78,7 +90,7 @@ Check the results using `less ${HOME}/clair3_ont_quickDemo/output/merge_output.v

## Installation

### Option 1. Docker pre-built image (recommended)
### Option 1. Docker pre-built image

A pre-built docker image is available [here](https://hub.docker.com/layers/hkubal/clair3/latest/images/sha256-769a241a9e1aab422d7309022ab14e8982d1e2af32c24ee7c16230c24b52cd74?context=explore). With it you can run Clair3 using a single command:

Expand All @@ -103,7 +115,28 @@ docker run -it \

Check [Usage](#Usage) for more options.

### Option 2. Docker Dockerfile
### Option 2. Singularity

```bash
conda config --add channels defaults
conda create -n singularity-env -c conda-forge singularity -y
conda activate singularity-env

# singularity pull docker pre-built image
singularity pull docker://hkubal/clair3:v0.1-r1

# run clair3 like this afterward
singularity exec clair3_v0.1-r1.sif \
/opt/bin/run_clair3.sh \
--bam_fn=${INPUT_DIR}/input.bam \ ## change your bam file name here
--ref_fn=${INPUT_DIR}/ref.fa \ ## change your reference name here
--threads=${THREADS} \ ## maximum threads to be used
--platform="ont" \ ## options: {ont,hifi,ilmn}
--model_path="/opt/models/ont" \ ## absolute model path prefix, change platform accordingly
--output=${OUTPUT_DIR} ## absolute output path prefix
```

### Option 3. Docker Dockerfile

```bash
# clone Clair3
Expand All @@ -118,7 +151,7 @@ docker build -f ./Dockerfile -t hkubal/clair3:v0.1 .
docker run -it hkubal/clair3:v0.1 /opt/bin/run_clair3.sh --help
```

### Option 3. Build an anaconda virtual environment
### Option 4. Build an anaconda virtual environment

**Anaconda install**:

Expand Down Expand Up @@ -172,30 +205,7 @@ tar -zxvf clair3_models.tar.gz -C ./models
--output=${OUTPUT_DIR} ## absolute output path prefix
```

### Option 4. Singularity

```bash
conda config --add channels defaults
conda create -n singularity-env -c conda-forge singularity -y
conda activate singularity-env

# singularity pull docker pre-built image
singularity pull docker://hkubal/clair3:v0.1-r1

# run clair3 like this afterward
singularity exec clair3_v0.1-r1.sif \
/opt/bin/run_clair3.sh \
--bam_fn=${INPUT_DIR}/input.bam \ ## change your bam file name here
--ref_fn=${INPUT_DIR}/ref.fa \ ## change your reference name here
--threads=${THREADS} \ ## maximum threads to be used
--platform="ont" \ ## options: {ont,hifi,ilmn}
--model_path="/opt/models/ont" \ ## absolute model path prefix, change platform accordingly
--output=${OUTPUT_DIR} ## absolute output path prefix
```

----


---

## Usage

Expand Down