AutoHiC is a deep learning tool that uses Hi-C data to support genome assembly.
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The latest information about AutoHiC is available via https://github.com/Jwindler/AutoHiC
We provide a container that wraps the dependencies needed to run an AutoHiC analysis. This streamlines setup and installation, and makes it easy to keep track of all software versions used in the analyses. It guarantees that only dependency versions compatible with AutoHiC are used.
See the Docker userguide for details. Here are suggested examples of how to use the AutoHiC container in the interactive mode. For more detailed AutoHiC usage, see the dedicated section below.
# pull images
docker pull jwindler/autohic:main
# start container
docker run -it -v $(pwd):/home/autohic jwindler/autohic:main bash
# You need to use mounts (-v) to exchange files between the host filesystem on which your user can write and the container filesystem. ( Default "./" )
# clone AutoHiC
git clone https://github.com/Jwindler/AutoHiC.git
# cd AutoHiC
cd AutoHiC
# activate AutoHiC
conda activate autohic
# Prepare genomic data, Hi-C data and modify configuration files...
# Please refer to https://github.com/Jwindler/AutoHiC#data-preparation
# run
nohup python3.9 autohic.py -c cfg-autohic.txt > log.txt 2>&1 &
Content type
Image
Digest
sha256:a529c1cf7…
Size
6 GB
Last updated
about 3 years ago
docker pull jwindler/autohic:main