Docker image for OpenRDP

brj1 commented 1 year ago

Here the fork of my Dockerfile for OpenRDP. It uses a debian base with python already installed (python:3.8-slim).

I couldn't get the command line to work well, so you have to pipe the input and out files through docker. I also had to rebuild the binaries for 3Seq and GENECONV (they might be using different versions from this repo); this is handled inside the Dockerfile.

To build: docker build -t openrdp .

To run: cat alignment.fasta > docker run -i --rm openrdp > output.csv

You may to sudo into these.

Since you must pipe the input, you cannot change the config file or specify which tests are done (I copied "tests/test.cfg" and let it run all tests), once the container is built. docker's OpenRDP will use the file "docker/docker.cfg" for its config file. If you want a different config file, you can edit "docker/docker.cfg" and then rebuild the docker image. You can also change the parameters in line 54 of the Dockerfile to limit the tests used.

ArtPoon commented 1 year ago

@GopiGugan can you confirm that you can build this image before we merge this PR?

GopiGugan commented 1 year ago

$ docker build . -t openrdp
[+] Building 114.6s (15/15) FINISHED
...
$ docker images
REPOSITORY   TAG       IMAGE ID       CREATED         SIZE
openrdp      latest    acd3763cc14e   2 minutes ago   1.23GB
$ cat tests/CRF_07_test.fasta | docker run -i --rm openrdp > output.csv
Loading configuration from /app/cfg.ini
Starting 3Seq Analysis
Finished 3Seq Analysis
Starting GENECONV Analysis
Finished GENECONV Analysis
Setting up bootscan analysis...
Starting Scanning Phase of Bootscan/Recscan
Finished Scanning Phase of Bootscan/Recscan
Setting up maxchi analysis...
Setting up siscan analysis...
Setting up chimaera analysis...
Setting up rdp analysis...
Scanning triplet 0 / 1
Scanning triplet 1 / 1

Method      Start   End Recombinant Parent1 Parent2 Pvalue
------------------------------------------------------------------------
Geneconv    8972    9114    B           07_BC   -       0.00E+00
Geneconv    4416    5139    C           07_BC   -       1.17E-03
Geneconv    5927    5957    B           07_BC   -       9.04E-03
Geneconv    8219    8322    C           07_BC   -       3.10E-02
Geneconv    8972    9118    C           -       -       0.00E+00
...

Was able to build the image
We should document how to use this docker image in the README after merging into dev

PoonLab / OpenRDP

Docker image for OpenRDP #50