Creating a Singularity recipe #32
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…admir Fonov's Minc Tools 1.9.16 image on singularity hub. It currently installs: 1. ANTS 2. Java 3. Bpipe It has been tested up to a point where it was looking for quaratine.
shots47s
changed the title
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Thanks for the initial skeleton. A few things to start: After that, it looks like the container has at least the base mni models and beast-library-1.1, which is most of the QUARANTINE_PATH contents, probably just need to do some symlinking tricks to create the right paths. |
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Ah, good to know, that would have made things easier. Minc-stuffs was a bit of a residual from another project. |
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As far as installing bpipe, untarring the release tarball is quicker/easier and then we'll have a stamped version as well: https://github.com/ssadedin/bpipe/releases |
…loading Bpipe from tarball and pulling the minc-bpipe-library to the image.
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Ok, I have modified the Singularity image, when I follow the run procedure on the README.md by running: bpipe run -n 4 /minc-bpipe-library/pipeline.bpipe ./MRI_Image.mnc In short, it is looking for qsub. For it to run in Singularity, we should customize to run locally, as it will run in the image. So what would be the next steps then. Modifying the bpipe.config? |
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For a containerized image, you can just delete bpipe.config |
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Ok, great, I have added removing this file to the container, when I run the command now, I get a quick return. The .bpipe directory is created, and nothing seems to be happening. How should we debug now, I can send by email my logs or I can post the log here (although may clog things up). |
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Don't mind clogging up github, its not my email inbox :) |
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Ok, here is what I get in the logs: |
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Here is my command.log: |
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Okay, so, before going over this any further, I'm going to add a clearer dependencies list to the README. Expect it coming. |
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Hi @shots47s I added a much clearer description of dependencies at https://github.com/CobraLab/minc-bpipe-library#installation-dependencies Can you take a look and see how much effort it is to bring in the extra dependencies? The only other problem with this is that pathing is a bit hard-coded right now according to the CIC quarantine structure, see https://github.com/CobraLab/minc-bpipe-library/blob/master/minc-library.bpipe#L1-L33 I have to address that with: #27 |
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I will work to update the recipe, but at first glance, bringing these in should not be a problem as long as the recipe has access to their locations. Hard coding the path within the container should be easy, we can just add the env variable to the recipe. |
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I agree for a container hard-coding is fine, but in general I'd like to increase the flexibility to use the ADNI or pediatric templates (if your subjects are pediatric) and making this externally settable is ideal. Also, in terms of non-container use, hard-coding makes things more difficult than it should be. |
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Yep, completely agree with you. |
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Hi @shots47s have you had a chance to address the dependencies updates I made? |
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Hi, Following up here, anything I can help with? I'm planning changing to a config-file based setup conditional on a bug being fixed at the bpipe level. |
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Thanks gdevenyi, got buried under other things, I will get back to this soon. Am I holding up your changes? |
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No, just warning you that there will be a config change coming when the bug is addressed. If it happens after the recipe I'll make sure it stays working. |
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Hello, if I understand correctly @shots47s was working on a singularity recipe for minc-bpipe-library, is this correct? If so, is the singularity recipe available somewhere? We are having lots of issues with minc-bpipe-library dependencies and would really benefit from such a recipe. Or, even better, a docker or singularity image? Thanks! |
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I wrote my own Dockerfile here, https://github.com/CoBrALab/MAGeTDocker for another project which includes minc-bpipe-library which runs fine as a singularity image. Just open a shall in the container and run as a basic bpipe pipeline. |
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ok thanks! |
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Added initial and currently incomplete Singularity recipe based on Vladmir Fonov's Minc Tools 1.9.16 image on singularity hub. It currently installs:
It has been tested up to a point where it was looking for quarantine.