running docker image problem about arpeggio HOT 6 CLOSED

Hi Thomas,

Thanks for your interest in Arpeggio.

Unfortunately the original web server address is down, but Dr David Ascher kindly runs a mirror at the University of Melbourne:

http://biosig.unimelb.edu.au/arpeggioweb/

If you'd still like to run using Docker: I'm currently on the road so not able to test this right away.

From a quick Google, this may be a Docker engine bug. You could try removing an existing Arpeggio containers (if any) and restarting Docker and trying again.

If that doesn't work, you could remove the part of the run command mapping the user in the Docker container to your Mac user (-u `id -u`:`id -g). The output files would then be owned by root, but (assuming you have sudo capability) could then be changed to be owned by your user after running, using chown.

Hope that's helpful. Let me know if it still proves to be an issue and I'll see if I can reproduce this issue.

All the best,

Harry

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Hi Harry,

Many thanks for the prompt reply and the link to the mirror. I would still like to get arpeggio running with Docker, but I ran into more problems, some of which I have solved, but one which I still cannot. Removing the user mapping from the run command solved the problem and I was able to run arpeggio on a test pdb file and generate the output files successfully without building the docker image, but I would like to benefit from the graphical visualisation and export to PyMOL features, which presumably I can do through the Docker container? I have created the Dockerfile in a subdirectory of my home directory, since executing docker build in my home directory gives an error message. I can now execute docker build -t 'arpeggio' . but it fails part way through with the following error message:

leonart3@a743-th-macbook arpeggio % docker build -t 'arpeggio' .
Sending build context to Docker daemon 2.048kB
Step 1/9 : FROM harryjubb/openbabel-python:python2.7.15
---> c4b19add1fd4
Step 2/9 : LABEL maintainer="Harry Jubb[email protected]"
---> Using cache
---> e9e3ea9ca8cf
Step 3/9 : RUN mkdir /arpeggio
---> Using cache
---> 6fd63fc77dd7
Step 4/9 : WORKDIR /arpeggio
---> Using cache
---> c56b923a5314
Step 5/9 : COPY requirements.txt /arpeggio
COPY failed: stat /var/lib/docker/tmp/docker-builder084371147/requirements.txt: no such file or directory

I'm afraid this may read very much like I haven't a clue what is going on here, which is fairly close to the truth, so I very much appreciate your help!

Best,
Thomas

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Hi Thomas,

The public image pushed to Dockerhub contains the show_contacts.py script, so it may be easier to use that rather than building locally: https://github.com/harryjubb/arpeggio#using-the-public-docker-image

It looks like the reason the local build is failing is that (correct me if I'm wrong), it's just the Dockerfile without the rest of the repository? The Dockerfile copies files from the repository into the Docker image. To build locally you'd need to clone the repository locally and run the build inside your clone of the repository.

The public image is up-to-date (at least as far as the code is here), so I'd recommend that route first. To run the contacts script you'd replace arpeggio.py with show_contacts.py. Adding the -h flag shows the options available. I'd expect the XML-RPC PyMOL connection probably won't work within Docker out-of-the-box, but saving a PyMOL script should work.

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Hi Thomas,

it seems to be like pymol, but not quite the same

Very true! The selection parser is a little limited I'm afraid, however:

arpeggio will not take the syntax /A/315-321/ as a selection. It will take individual amino acids or the whole chain, but not just part. I obviously don’t want all the contacts from the folded domain, just the ones at the interface. How can I make arpeggio map only the interface?

You should be able to specify multiple -s options to define your interface, e.g. -s /A/315/ -s /A/316/ -s /A/317/ -s /A/318/ -s /A/319/ -s /A/320/ -s /A/321/

Is there a manual or something somewhere that can help me?

There is no explicit manual unfortunately. I've tried to put the key information into the paper and supplementary materials, README with FAQs, and some things have been answered in GitHub issues and moved into the FAQs. I'll add the multiple selection syntax to the README.

I'm not actively maintaining the project at this time but happy to answer questions as best as I can. I'd also recommend looking at PDBe's fork. Lukas Pravda from the EBI has done a fantastic job of modernising and modularising the code, including support for mmCIF if that is helpful.

https://github.com/PDBeurope/arpeggio

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