sc3D-Browser
sc3D-Browser is a viewer for single-cell and 3D chromatin genomic data, originally designed to demonstrate multi-modal data sets. sc3D is built on Django web framework to support rapid, secure and stable service. And the complete workflow is here.
Installation
1. Install docker and load docker image
git clone https://github.com/Tomos-cell/sc3D-Browser docker pull sdas124v/sc3d_django docker pull sdas124v/sc3d_nginx
2. Run sc3D-Browser container (for mac or linux user)
db="/d/desktop/database" // the absolute path of database folder
ip="localhost" // input "localhost" to run locally or IP to run remotely
nproc=8 // according to your cpu number
docker network create sc3d_network --driver bridge
docker run -d --name sc3d_django_container --security-opt seccomp=unconfined --restart always --volume ${db}:/app/database --expose 8001 -e DJANGO_ALLOWED_HOSTS=${ip} -e DB=${db} -e UWSGI_PROCESSES=${nproc} -e OPENBLAS_NUM_THREADS=${nproc} --network sc3d_network sc3d_django
docker run -d --name sc3d_nginx_container --restart always -p 8788:80 --volume ${db}/cifdata:/app/database/cifdata --network sc3d_network sc3d_nginx
docker exec -it sc3d_django_container python manage.py makemigrations
docker exec -it sc3d_django_container python manage.py migrate
(for windows user)
$db="D:\desktop\database" // the absolute path of database folder
$ip="localhost" // input "localhost" to run locally or IP to run remotely
$nproc=8 // according to your cpu number
docker network create sc3d_network --driver bridge
docker run -d --name sc3d_django_container --security-opt seccomp=unconfined --restart always --volume ${db}:/app/database --expose 8001 -e DJANGO_ALLOWED_HOSTS=${ip} -e DB=${db} -e UWSGI_PROCESSES=${nproc} -e OPENBLAS_NUM_THREADS=${nproc} --network sc3d_network sc3d_django
docker run -d --name sc3d_nginx_container --restart always -p 8788:80 --volume ${db}/cifdata:/app/database/cifdata --network sc3d_network sc3d_nginx
docker exec -it sc3d_django_container python manage.py makemigrations
docker exec -it sc3d_django_container python manage.py migrate
3. Access web
If you run it locally, please access at http://localhost:8989. If you run it remotely, please access http://ip:8989. If you need help about registering and uploading, please access http://ip:8989/doc.
Quick Start
0. Download docker, python(v3.7) by conda and prepare the file
docker cp sc3d_django_container:/app/upload2sqlite.py .
1. Register
python upload2sqlite.py createsuperuser
2. Upload genome (for mac or linux user)
python upload2sqlite.py addGenome -a $assembly -s $size -c $chrband -dir $db $assembly: genome assembly name, $size and $chrband: see example below, $db: /root/sc3DBrowser/database
### hg38.size chr1 248956422 chr2 242193529 chr3 198295559 ### hg38.chrband chr1 0 2300000 p36.33 gneg chr1 2300000 5300000 p36.32 gpos25 chr1 5300000 7100000 p36.31 gneg
3. Upload file
python upload2sqlite.py filecheck -i $input -a $assembly -l $upload -o list python upload2sqlite.py upload -i list -dir $db -u $user $input: input file or folder $assembly: genome assembly name $upload: name your upload folder $db: /root/sc3DBrowser/database $user: your user name
Tutorial
How to delete tracks
Firstly enter the Admin panel in Browser page, then check the box of tracks you want to delete, perform the "Delete selected tables" operation, and finally click the "Go" button.
How to modify tracks
Firstly enter Admin panel in Brower page, then click the track you want to modify, change the properties, finally click "Save" button.
API
Accepted Format
Contact
We welcome you to contact us if you have any problems in using sc3D!
Email : 12207142@zju.edu.cn