Docker image (for macOS)
EAGLE-RC
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.
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
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