campbio/sctk_shiny repository overview

⁠Single Cell TK

The Single Cell ToolKit (SCTK) is an analysis platform that provides an R interface to several popular scRNA-seq preprocessing, quality control, and visualization tools. SCTK imports raw or filtered counts from various single cell sequencing technologies and upstream tools such as 10x CellRanger, BUStools, Optimus, STARSolo, and more. By integrating several publicly available tools written in R as well as Python, SCTK performs extensive quality control measures including doublet detection and batch effect correction. Additionally, SCTK summarizes results and related visualizations in a comprehensive R markdown and/or HTML report. SCTK provides a standardized single cell analysis workflow by representing the counts data and the results using the SingleCellExperiment⁠ R object. Furthermore, SCTK enables seamless downstream analysis by exporting data and results in flat .txt and Python Anndata formats.

A comprehensive list of available functions is listed in the Reference section.

⁠Installation on Linux server

⁠System setup

⁠Step 1:

Check if the docker is installed on server by using following command:

docker -v

⁠Step 2:

If the docker is not installed then install it on server by using following command else skip this step:

sudo snap install docker

⁠Step 3:

Check if the docker service is running by using following command:

sudo service docker status

⁠Step 4:

If the docker service is not running then run it by using following command else skip this step:

sudo snap start docker

⁠Step 5:

Now it's time to take image pull from docker hub by using following command:

docker pull campbio/sctk_shiny:latest

Note: If you get permission denied error from server then use following command to grant required permission to docker and repeat Step 5:

sudo chmod 666 /var/run/docker.sock\

⁠Step 6:

Once the docker image is pulled from docker hub then check the list of images on server by using following command:

docker images

This will list down all the available docker images on server.

⁠Step 7:

Run the docker image by using following command:

docker run -d -p 80:80 campbio/sctk_shiny:latest

Note: The version name after the colon is the tag of docker image. If there is a new image then please use the latest tag name. On running this command successfully, shiny app can be accessed by using domain name or server ip address. If there is any error of missing dependency then please install the missing dependency and follow step 7 again. If needed, the following command can be used to install httpd Apache (and follow step 7 again):

sudo snap install httpd

⁠Step 8 (Final Step):

Once the docker container starts running, configure it to restart automatically as the docker container will stop running on app crash and shiny app will no longer be available for users. Following command will list down all running containers.

docker ps -a

Copy the container id and use following command to configure it for auto restart.

docker update --restart unless-stopped CONTAINER_ID_HERE

⁠Now the shiny app is running on your server.