# CustardPy: Docker image for 3D genome analysis
<img src = "image/CustardPy.jpg" width = 700ptx>
This repository contains
- Source code of **CustardPy** (PyPI),
- Dockerfile of **CustardPy** Docker image,
- [Full Manual](https://custardpy.readthedocs.io), and
- Tutorial data of Hi-C and Micro-C analysis using demo data.
## 0. Changelog
See [Changelog](https://github.com/rnakato/CustardPy/blob/main/ChangeLog.md)
## 1. Installation
Docker image is available at [DockerHub](https://hub.docker.com/r/rnakato/custardpy).
### 1.1 Docker
To use the docker command, type:
# Pull docker image
docker pull rnakato/custardpy
# Container login
docker run --rm -it rnakato/custardpy /bin/bash
# Execute a command
docker run --rm -it -v (your directory):/opt/work rnakato/custardpy <command>
When calling loops using Juicer HICCUPS, supply the ``--gpus all`` option to allow GPU computation (GPU card needed):
docker run --gpus all -it --rm -it -v (your directory):/opt/work rnakato/custardpy call_HiCCUPS.sh
- user:password
- ubuntu:ubuntu
### 1.2 Singularity
Singularity is the alternative way to use CustardPy.
With this command you can build the singularity file (.sif) of CustardPy:
singularity build custardpy.sif docker://rnakato/custardpy
Instead, you can download the CustardPy singularity image from our [Dropbox](https://www.dropbox.com/scl/fo/lptb68dirr9wcncy77wsv/h?rlkey=whhcaxuvxd1cz4fqoeyzy63bf&dl=0) (We use singularity version 3.8.5).
Then you can run CustardPy with the command:
singularity exec custardpy.sif <command>
Singularity will automatically mount the current directory. If you want to access the files in the other directory, use the `--bind` option, for instance:
singularity exec --bind /work custardpy.sif <command>
This command mounts the `/work` directory.
When calling loops using Juicer HICCUPS, supply ``--nv`` option to allow GPU computation (GPU card needed):
singularity exec --bind /work custardpy.sif call_HiCCUPS.sh
## 2. Quickstart
# download Churros/tutorial directory
git clone https://github.com/rnakato/CustardPy.git
cd CustardPy/tutorial/Hi-C/
# download fastq and genome data and make index
bash 00_getdata.sh
# Execute Juicer pipeline
bash QuickStart_juicer.sh
## 3. Usage
See https://custardpy.readthedocs.io for the detailed Manual.
## 4. Build Docker image from Dockerfile
First clone and move to the repository
git clone https://github.com/rnakato/CustardPy.git
cd CustardPy/Docker
Then type:
docker build -f Dokerfile.<version> -t <account>/custardpy_juicer .
## 6. Reference
- Nakato R, Sakata T, Wang J, Nagai LAE, Nagaoka Y, Oba GM, Bando M, Shirahige K, Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors, *Nature Communications*, 2023. doi: [10.1038/s41467-023-41316-4](https://www.nature.com/articles/s41467-023-41316-4)
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"description": "# CustardPy: Docker image for 3D genome analysis\n\n<img src = \"image/CustardPy.jpg\" width = 700ptx>\n\nThis repository contains\n- Source code of **CustardPy** (PyPI),\n- Dockerfile of **CustardPy** Docker image, \n- [Full Manual](https://custardpy.readthedocs.io), and\n- Tutorial data of Hi-C and Micro-C analysis using demo data.\n\n## 0. Changelog\n\nSee [Changelog](https://github.com/rnakato/CustardPy/blob/main/ChangeLog.md)\n\n## 1. Installation\n\nDocker image is available at [DockerHub](https://hub.docker.com/r/rnakato/custardpy).\n\n### 1.1 Docker\n\nTo use the docker command, type:\n\n # Pull docker image\n docker pull rnakato/custardpy\n\n # Container login\n docker run --rm -it rnakato/custardpy /bin/bash\n # Execute a command\n docker run --rm -it -v (your directory):/opt/work rnakato/custardpy <command>\n\nWhen calling loops using Juicer HICCUPS, supply the ``--gpus all`` option to allow GPU computation (GPU card needed):\n\n docker run --gpus all -it --rm -it -v (your directory):/opt/work rnakato/custardpy call_HiCCUPS.sh\n\n- user:password\n - ubuntu:ubuntu\n\n### 1.2 Singularity\n\nSingularity is the alternative way to use CustardPy.\nWith this command you can build the singularity file (.sif) of CustardPy:\n\n singularity build custardpy.sif docker://rnakato/custardpy\n \nInstead, you can download the CustardPy singularity image from our [Dropbox](https://www.dropbox.com/scl/fo/lptb68dirr9wcncy77wsv/h?rlkey=whhcaxuvxd1cz4fqoeyzy63bf&dl=0) (We use singularity version 3.8.5).\n\nThen you can run CustardPy with the command:\n\n singularity exec custardpy.sif <command>\n\nSingularity will automatically mount the current directory. If you want to access the files in the other directory, use the `--bind` option, for instance:\n\n singularity exec --bind /work custardpy.sif <command>\n\nThis command mounts the `/work` directory.\n\nWhen calling loops using Juicer HICCUPS, supply ``--nv`` option to allow GPU computation (GPU card needed):\n\n singularity exec --bind /work custardpy.sif call_HiCCUPS.sh\n\n## 2. Quickstart\n\n # download Churros/tutorial directory\n git clone https://github.com/rnakato/CustardPy.git\n cd CustardPy/tutorial/Hi-C/\n\n # download fastq and genome data and make index\n bash 00_getdata.sh\n\n # Execute Juicer pipeline\n bash QuickStart_juicer.sh\n\n## 3. Usage\n\nSee https://custardpy.readthedocs.io for the detailed Manual.\n\n## 4. Build Docker image from Dockerfile\n\nFirst clone and move to the repository\n\n git clone https://github.com/rnakato/CustardPy.git\n cd CustardPy/Docker\n\nThen type:\n\n docker build -f Dokerfile.<version> -t <account>/custardpy_juicer .\n\n## 6. Reference\n\n- Nakato R, Sakata T, Wang J, Nagai LAE, Nagaoka Y, Oba GM, Bando M, Shirahige K, Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors, *Nature Communications*, 2023. doi: [10.1038/s41467-023-41316-4](https://www.nature.com/articles/s41467-023-41316-4)\n",
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