masaomi / eaglerc_example_2021

EAGLERC_example_2021

Docker image (for macOS)

• https://hub.docker.com/r/masaomi/eaglerc

EAGLE-RC

• https://github.com/tony-kuo/eagle

Reference (Citation)

• Tony Kuo and Martin C Frith and Jun Sese and Paul Horton. EAGLE: Explicit Alternative Genome Likelihood Evaluator. BMC Medical Genomics. 11(Suppl 2):28. https://doi.org/10.1186/s12920-018-0342-1
• Tony C Y Kuo, Masaomi Hatakeyama, Toshiaki Tameshige, Kentaro K Shimizu, Jun Sese Briefings in Bioinformatics, Volume 21, Issue 2, March 2020, Pages 395–407, https://doi.org/10.1093/bib/bby121

Note

• You need to install Docker engine in your environment in advance of the following commands execution.

macOS

How to set up the Docker image and container:

$ docker pull masaomi/eaglerc
$ docker run -it --workdir=/root --name eaglerc masaomi/eaglerc

How to run the test code of EAGLE-RC (in the Docker container)

# sh scripts/test_eaglerc.sh

After a while, some programs run, which will take a few minutes, and you will get the result:

Executing EAGLE-RC...

Done

Without EAGLE-RC (direct alignment)
#Ahal reads mapped to Ahal reference: 67059
#Alyr reads mapped to Alyr reference: 99077
#Akam reads mapped to Akam reference: 166136
#Mis-mapped reads of Akam reads to Akam reference: 1680

By EAGLE-RC (read classification)
#Akam reads mapped to Ahal reference after EAGLE-RC: 65153
#Akam reads mapped to Alyr reference after EAGLE-RC: 97120
#Mis-mapped reads of Akam reads to Ahal reference after EAGLE-RC: 248
#Mis-mapped reads of Akam reads to Alyr reference after EAGLE-RC: 219

other OS (Linux, Windows)

Note

• Please build the Docker image from the Dockerfile

$ git clone https://github.com/masaomi/EAGLERC_example_2021.git
$ cd EAGLERC_example_2021/
$ docker build . --tag masaomi/eaglerc
(it will take some minutes)
$ docker run -it --workdir=/root --name eaglerc masaomi/eaglerc

Note

• Once you exit from the Docker container, the container will stop
• Please start it again by

$ docker container start eaglerc

and login to the container

$ docker exec -it --user root eaglerc bash

For more details about Docker commands, please ask Google