pskolekar/sequencerr repository overview

⁠Docker image for Supplementary data and codes for

⁠SequencErr: measuring and suppressing sequencer errors in next generation sequencing

Eric M Davis^*1, Yu Sun^*1,2, Yanling Liu^*1, Pandurang Kolekar¹, Ying Shao¹, Karol Szlachta¹, Heather L Mulder¹, Dongren Ren³, Stephen V Rice¹, Zhaoming Wang⁴, Joy Nakitandwe⁵, Alex Gout¹, Leslie L Robison⁴, Stanley Pounds⁶, Jefferey Klco⁵, John Easton¹, Xiaotu Ma^1#

• ¹ Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN

• ² Department of Computer Science, University of Memphis, Memphis, TN

• ³ Independent Researcher, Memphis, TN

• ⁴ Department of Epidemiology & Cancer Control, St. Jude Children's Research Hospital, Memphis, TN

• ⁵ Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN

• ⁶ Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN

• # To whom correspondence should be addressed: [email protected]⁠

⁠SequencErr

SequencErr app is available on St. Jude Cloud at https://platform.dnanexus.com/app/sequencerr⁠ for non-profit research uses.

⁠Usage

⁠Pull the image

docker pull pskolekar/sequencerr:rstudio-v3.6

⁠Run the container with RStudio pointing to Supplementary data folder for SequencErr

docker run --rm -p 127.0.0.1:8787:8787 -e DISABLE_AUTH=true pskolekar/sequencerr:rstudio-v3.6 init

⁠Open the following URL in any browser to perform any R related operations on data in the RStudio

http://localhost:8787/⁠

⁠Stop the container

To stop the container open a new terminal and get the container ID for above running container and execute following command in the new terminal

docker ps -a

docker stop <container-ID>