How to run EDEN without GUI

eden_without_gui.sh

### description to run EDEN without the GUI, please be aware that some check routines are implemented inside the GUI and thus will not applied to the data (for example the check for validity of input files)
### commands that must be executed inside the docker container are written as `eden@4d4a16919ce0:~$ command`

# 1. run docker using the interactive mode
sudo docker run -p 80:3838 -i -t --entrypoint /bin/bash philippmuench/eden
eden@4d4a16919ce0:~$ mkdir /home/eden/data/fasta
# now the console inside the docker container should be visible `eden@4d4a16919ce0:~$`. This contains also the number of the docker instance, you should use this number for the following commands. If you get the Error "docker: Error response from daemon: driver failed programming external connectivity on endpoint jovial_jenning" please shutdown the running docker instance first. You can do this by usind `sudo docker ps` followed by 'sudo docker stop 4d4a16919ce0' (the last number is the instance ID, please use the instance ID showed after 'sudo docker ps')

# 2a) (optional) using .fasta files of your contigs
#copy you data manually inside the docker container. For this please open a new terminal window. Suppose the fasta files are locaded at /path_to_folder/*.fasta and the docker instance ID is 4d4a16919ce0 (please use your own docker instance ID)
sudo docker cp /path_to_folder/file_1.fasta 4d4a16919ce0:/home/eden/data/fasta/
sudo docker cp /path_to_folder/file_2.fasta 4d4a16919ce0:/home/eden/data/fasta/

# 2b) in case you want to use ORF files instead of .fasta files, copy faa anf ffn files for each sample in the corresponding folders
sudo docker cp /path_to_folder/file_1.faa 4d4a16919ce0:/home/eden/data/faa/
sudo docker cp /path_to_folder/file_1.ffn 4d4a16919ce0:/home/eden/data/ffn/

# 3) you can upload a HMM model. If you don't upload the model.hmm EDEN will automatically download and use the TIGRFAM hmm model
sudo docker cp /path_to_folder/model.hmm 4d4a16919ce0:/home/eden/data/model.hmm

# 4) you can upload a samples.txt file if you want group the samples
# this file should have the same format like this example sample file at https://github.com/philippmuench/eden/blob/master/sample_files/samples.txt (list of fasta names without extention seperated by '+')
# if you dont upload this files, all samples will be grouped together
sudo docker cp /path_to_folder/samples.txt 4d4a16919ce0:/home/eden/data/samples.txt

# 5) start eden
# the first number is the number of CPUs used for the analysis while the second number is the gap threshold. You may want to change name_of_eden_run to a other random name
eden@4d4a16919ce0:~$ /home/eden/start_check.sh /home/eden/data/faa /home/eden/data/ffn 4 name_of_eden_run 0.8 /home/eden/data/model.hmm /home/eden/data/samples.txt

# 6) (optinal) visualize results
eden@4d4a16919ce0:~$ /home/eden/start_server.sh
# and point the browser to localhost, the new files will be imported on startup. Please be aware that after you shut down the server the clean up routine will remove all input files (the /home/eden/data/tar folder will be unaffected). You can stop the server using Control+C

# 7) (optional) copy raw results to your local machine
sudo docker cp 4d4a16919ce0:/home/eden/data/tar/name_of_eden_run.tar /local_folder/my_eden_run.tar