Read in ODGI Bin output and identify co-linear components
Environment: Anaconda 3.7
Ggfapy etc. does not have an anaconda package, so it's necessary to use pip:
pip install -r requirements.txt
IDE: Pycharm Professional 2019.1
- Travis CI - automatically runs tests on master and development branches
Parameters: --json-file=data/run1.B1phi1.i1.seqwish.w100.json --out-folder=data/ --cells-per-file=5000
Some of the dependencies requires c compiler (gcc on Linux). On Debian derived Linux distributions (e.g. Debian, Ubuntu), it is recommended to do
sudo apt-get update
sudo apt-get install -y build-essential
Then go to the package directory and run (note the dot at the end)
pip install .
It should install script segmentation.py. So, to run it in command line just run
segmentation.py --json-file=/path/to/your/json/files --out-folder=/output/directory/path
To get the full list of parameters, run the script without any parameters.
This module can be run in Docker. To build an image, run:
docker build -t component_segmentation:latest .
After the image is build, to run component_segmentation, use the following command:
docker run --rm -it -v <full/path/to/data>:/data component_segmentation:latest --json-file=/data/your.json.file.json --out-folder=/data/out
If several files with common prefix your.json.files.prefix should be processed, run
docker run --rm -it -v <full/path/to/data>:/data component_segmentation:latest --json-file=/data/your.json.files.prefix"*" --out-folder=/data/out
Other options can be added at the end. To get the full option list, run container without any extra options as:
docker run --rm -it component_segmentation:latest