sonm/task-r-rnaseq repository overview

⁠RNA-sequencing by SONM

This is R implementation of bioniformatics case named single cell RNA-sequencing . All materials (dataset, codebase, lib importing) are ready as well, you just need to run the attached script. If you are interested in understandig what is going on, visit:

• What is rna-seq⁠
• [Single cell](https://en.wikipedia.org/wiki/Single_cell_sequencing#Single-cell_RNA_sequencing_(scRNA-seq)⁠
• Pubmed article⁠

⁠Quickstart

docker run -d -p 8787:8787 sonm/task-r-rnaseq:latest

Visit localhost:8787 in your browser and log in with username:password as rstudio:rstudio.

⁠Note:

• We are using rocker/rstudio-stable:3.4.5
• Dataset source: 10xgenomix⁠ conrete⁠

⁠Use a custom password by specifying the PASSWORD environmental variable

docker run -d -p 8787:8787 -e PASSWORD=yourpasswordhere rocker/rstudio

⁠Give the user root permissions (add to sudoers)

docker run -d -p 8787:8787 -e ROOT=TRUE rocker/rstudio

Link a local volume (in this example, the current working directory, $(pwd)) to the rstudio container:

docker run -d -p 8787:8787 -v $(pwd):/home/rstudio rocker/rstudio

⁠Access a root shell for a running rstudio container instance

First, determine the name or id of your container (unless you provided a --name to docker run) using docker ps. You need just enough of the hash id to be unique, e.g. the first 3 letters/numbers. Then exec into the container for an interactive session:

docker exec -ti <CONTAINER_ID> bash

You can now perform maintenance operations requiring root behavior such as apt-get, adding/removing users, etc.

⁠Additional configuration options

• Custom user name: -e USER=<CUSTOM_NAME>
• Custom user id, group id, UMASK: -e USERID=<UID>, -e GROUPID=<GID>, e UMASK=022

Custom uid/gid etc is usually only needed when sharing a local volume for a user/group whose id does not match the default (1000:1000). Failing to do this could make files change permissions on the linked volume when accessed from RStudio.

Adding additional users: From a root bash shell (see above), the usual debian linux commands can be used to create new users and passwords, e.g.