just a simple tool that generates a circos plot from a bunch of fasta files
- the input files schould be named like
$genome_$sample.fastaand the input fasta files should have the following header formt:>contig-$number - clone this repo
git clone https://github.com/philippmuench/Donut.git - put your fasta (one or multipe) files in the
data/genomes/folder - add your Hidden Markov model file to
data/hmm/model.hmm - start the docker container
docker run -v /absolute/path/to/data/folder:/data philippmuench/donut - inspect the output written to
data/output/
from outer to inner:
- GC content
- gene density (black), hypothetical gene density (red)
- match to HMM models against ORFs
- links: similar ORF by blast
- colored links: similar ORFs that cover full a HMM match
comment the entrypoint in Dockerfile out than build the docker image from scatch
sudo docker build -t donut .
then start in interactive mode
sudo docker run -it -v /home/pmuench/github.com/philippmuench/easycircos/data:/data donut
inside the docker image start the tool
./start.sh
The error print to screen are not critical, becaused the hmmvis tool tries to export png image to the screen which is not possible within docker.
You can also change data/config/circos.config file from outside the container (because its mounted to the image) and run the circos step only to update the output file
./start_circos.sh