08-circos

Estimated time: 15 minutes

Example for circos

Change directory into the circos directory.

BASH

cd /projects/my-lab/08-circos

Verify nothing is in the directory

BASH

ls -lF

Make a circos SIF file by pulling the docker image circos.

BASH

singularity pull docker://alexcoppe/circos

Download the circos tutorial.

BASH

wget http://circos.ca/distribution/circos-tutorials-current.tgz

Untar and gzip the downloaded file.

BASH

tar xzvf circos-tutorials-current.tgz

BASH

ls -1F

OUTPUT

circos_latest.sif*
circos-tutorials-0.67/
circos-tutorials-current.tgz

Run tutorial 1/1

BASH

singularity exec -B $PWD circos_latest.sif /opt/circos/bin/circos -conf circos-tutorials-0.67/tutorials/1/1/circos.conf

The base image of the human chromosomes was created

circos_1_1

Run tutorial 8/6 histograms

BASH

singularity exec -B $PWD circos_latest.sif /opt/circos/bin/circos -conf circos-tutorials-0.67/tutorials/8/6/circos.conf

An image with histograms

circos_8_6

Run tutorial 8/11 links

BASH

singularity exec -B $PWD circos_latest.sif /opt/circos/bin/circos -conf circos-tutorials-0.67/tutorials/8/11/circos.conf

An image with links

circos_8_11

citations

http://circos.ca/