fastlbp-imbg 0.0.6

A wrapper for Ben's LBP bio pipeline

ImageTextureFinder

A project to create an easy-to-use way of finding areas of common patterns and structures within an image. Should work on any image, designed for use on any biological images including DAPI, IMC and H&E.

See sample_run.sh for details.

• Branch pip is the latest. It contains a pip packagable version of this project.
• Branch baseline is the most stable. It is not ready for pip tho.
• Branch dev is unstable and for dev purpuses only.

Container

Image tag is mkrooted/imbg-fastlbp. Hosted on Docker Hub (https://hub.docker.com/repository/docker/mkrooted/imbg-fastlbp/general). See Dockerfile for details.

Nextflow

The idea is to use mkrooted/imbg-fastlbp as execution environment. Note that Singularity should be used instead of default Docker. Nextflow can convert Docker container to a Singularity one automatically.

See main.nf for details. Unfinished though.

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Guides

How to build and deploy a pip package

Src: https://packaging.python.org/en/latest/tutorials/packaging-projects/

• Add your access token to .pypirc

  # ~/.pypirc 
  [pypi]
    username = __token__
    password = pypi-TOKEN_FROM_YOUR_PYPI_SETTINGS_GOES_HERE
  

• Install prerequisites

  pip install --upgrade twine build
  

• Edit project version in pyproject.toml
• Build and upload the project

  cd src/fastlbp_imbg
  python -m build      # .whl and .gz output will be at ./dist directory
  python3 -m twine upload dist/*   # note that this can accidentally upload unneeded builds
  

How to build a docker container

cd src/container
docker build -t mkrooted/imbg-fastlbp .   # note the dot
# this can take a lot of time on local pc

How to run fastlbp_imbg inside docker manually

docker run -v /full/path/to/host/data/dir:data mkrooted/imbg-fastlbp \
    python -m fastlbp_imbg \
    # --stages=1 --imgname=img1.jpg  \
    # etc etc other parameters go here

• -v stands for volume attachment. it gives the container an access to the files on your host OS.
  Syntax: -v host_path:container_path
• mkrooted/imbg-fastlbp is image name. should be the same as in -t of a docker build
• everything after the first line is a command to run inside the container