This repository provides a sequence uploader for the COVID-19 Virtual Biohackathon's Public Sequence Resource project. There are two versions, one that runs on the command line and another that acts as web interface. You can use it to upload the genomes of SARS-CoV-2 samples to make them publicly and freely available to other researchers. For more information see the paper.
To get started, first install the uploader, and use the bh20-seq-uploader command to upload your data.
There are several ways to install the uploader. The most portable is with a virtualenv.
- Prepare your system. You need to make sure you have Python, and the ability to install modules such as
pycurlandpyopenssl. On Ubuntu 18.04, you can run:
sudo apt update
sudo apt install -y virtualenv git libcurl4-openssl-dev build-essential python3-dev libssl-dev- Create and enter your virtualenv. Go to some memorable directory and make and enter a virtualenv:
virtualenv --python python3 venv
. venv/bin/activateNote that you will need to repeat the . venv/bin/activate step from this directory to enter your virtualenv whenever you want to use the installed tool.
- Install the tool. Once in your virtualenv, install this project:
Install from PyPi:
pip3 install bh20-seq-uploaderInstall from git:
pip3 install git+https://github.com/arvados/bh20-seq-resource.git@master- Test the tool. Try running:
bh20-seq-uploader --helpIt should print some instructions about how to use the uploader.
Make sure you are in your virtualenv whenever you run the tool! If you ever can't run the tool, and your prompt doesn't say (venv), try going to the directory where you put the virtualenv and running . venv/bin/activate. It only works for the current terminal window; you will need to run it again if you open a new terminal.
If you don't want to have to enter a virtualenv every time you use the uploader, you can use the --user feature of pip3 to install the tool for your user.
- Prepare your system. Just as for the
virtualenvmethod, you need to install some dependencies. On Ubuntu 18.04, you can run:
sudo apt update
sudo apt install -y virtualenv git libcurl4-openssl-dev build-essential python3-dev libssl-dev- Install the tool. You can run:
pip3 install --user git+https://github.com/arvados/bh20-seq-resource.git@master- Make sure the tool is on your
PATH. Thepip3command will install the uploader in.local/bininside your home directory. Your shell may not know to look for commands there by default. To fix this for the terminal you currently have open, run:
export PATH=$PATH:$HOME/.local/binTo make this change permanent, assuming your shell is Bash, run:
echo 'export PATH=$PATH:$HOME/.local/bin' >>~/.bashrc- Test the tool. Try running:
bh20-seq-uploader --helpIt should print some instructions about how to use the uploader.
If you plan to contribute to the project, you may want to install an editable copy from source. With this method, changes to the source code are automatically reflected in the installed copy of the tool.
- Prepare your system. On Ubuntu 18.04, you can run:
sudo apt update
sudo apt install -y virtualenv git libcurl4-openssl-dev build-essential python3-dev libssl-dev- Clone and enter the repository. You can run:
git clone https://github.com/arvados/bh20-seq-resource.git
cd bh20-seq-resource- Create and enter a virtualenv. Go to some memorable directory and make and enter a virtualenv:
virtualenv --python python3 venv
. venv/bin/activateNote that you will need to repeat the . venv/bin/activate step from this directory to enter your virtualenv whenever you want to use the installed tool.
- Install the checked-out repository in editable mode. Once in your virtualenv, install with this special pip command:
pip3 install -e .- Test the tool. Try running:
bh20-seq-uploader --helpIt should print some instructions about how to use the uploader.
For running/developing the uploader with GNU Guix see INSTALL.md
Run the uploader with a FASTA or FASTQ file and accompanying metadata file in JSON or YAML:
bh20-seq-uploader example/metadata.yaml example/sequence.fastaIf the sample_id of your upload matches a sample already in PubSeq, it will be considered a new version and supercede the existing entry.
All these uploaded sequences are being fed into a workflow to generate a pangenome for the virus. You can replicate this workflow yourself.
An example is to get your SARS-CoV-2 sequences from GenBank in seqs.fa, and then run a series of commands
minimap2 -cx asm20 -X seqs.fa seqs.fa >seqs.paf
seqwish -s seqs.fa -p seqs.paf -g seqs.gfa
odgi build -g seqs.gfa -s -o seqs.odgi
odgi viz -i seqs.odgi -o seqs.png -x 4000 -y 500 -R -P 5Here we convert such a pipeline into the Common Workflow Language (CWL) and sources can be found here.
For more information on building pangenome models, see this wiki page.
This project comes with a simple web server that lets you use the sequence uploader from a browser. It will work as long as you install the packager with the web extra.
To run it locally:
virtualenv --python python3 venv
. venv/bin/activate
pip install -e ".[web]"
env FLASK_APP=bh20simplewebuploader/main.py flask run
Then visit http://127.0.0.1:5000/.
For production deployment, you can use gunicorn:
pip3 install gunicorn
gunicorn bh20simplewebuploader.main:app
This runs on http://127.0.0.1:8000/ by default, but can be adjusted with various gunicorn options.
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