Custardpy

- Modified `custardpy_cooler_HiC` and `custardpy_cooler_MicroC` to allow multiple FASTQ files
- Changed the name of output directory for `custardpy_juicer`, `custardpy_cooler_HiC`, and `custardpy_cooler_MicroC`
- Modified options of Pairtools according to the [tutorial](https://github.com/open2c/pairtools/blob/master/doc/examples/pairtools_walkthrough.ipynb)
- Added [python-FIREcaller](https://github.com/jakublipinski/python-FIREcaller)
- Added the restriction files of Cooler for various genome builds and enzymes (see the help of `custardpy_cooler_HiC`)
- Bug fix: Wrong PATH of pairsqc.py

- Added [3DChromatin_ReplicateQC](https://github.com/kundajelab/3DChromatin_ReplicateQC)
- Added `run_3DChromatin_ReplicateQC.sh` for executing 3DChromatin_ReplicateQC
- Updated `custardpy_cooler_HiC` and `custardpy_cooler_MicroC`

- Added [GENOVA](https://github.com/robinweide/GENOVA)
- Added `calculate_compartment_strength` command to calculate compartment strength
- Added [HiCUP](https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/)
- Bug fix of pairtools and numpy version conflict

- Added `DEG_boundary_analysis` command for TAD-proximity analysis
- Added `custardpy_clustering_boundary` command for clustering TAD boundaries
- Added `custardpy_differential_DRF` command for differential DRF analysis
- Added `calculate_compartment_strength` command for calculating compartment strength
- Bug fix in `makeEigen.sh`
- Changed name of `custardpy_mappingHiC` to `custardpy_cooler_HiC`
- Changed name of `custardpy_mappingMicroC` to `custardpy_cooler_MicroC`

- Major Release!
- Merged the GitHub repositories for CustardPy (this site) and [Docker_CustardPy](https://github.com/rnakato/Docker_CustardPy) into a single repository.
- Unified the Docker images for [CustardPy](https://hub.docker.com/r/rnakato/custardpy) and [CustardPy_Juicer](https://hub.docker.com/r/rnakato/custardpy_juicer). Version 1 of the [CustardPy](https://hub.docker.com/r/rnakato/custardpy) docker image now supports all analyses previously offered by CustardPy and CustardPy_Juicer, rendering the latter unnecessary.

- Docker Image Specifications:
- OS: Ubuntu 20.04
- CUDA: cuda11.0.3
- cuDNN: v8
- R: 4.3
- Python: 3.9.13
- OpenJDK v17
- Juicer v1.6
- Juicer tools v1.22.01

Note: CustardPy does not support Juicer Tools v2 due to incompatibility with the ``.cool`` file format.

- Added tools
- [GENOVA](https://github.com/robinweide/GENOVA)
- [CHESS](https://chess-hic.readthedocs.io/en/latest/index.html)
- [FIREcaller](https://github.com/yycunc/FIREcaller)
- [STRIPENN](https://github.com/VahediLab/stripenn)
- [HiC-Pro](https://github.com/nservant/HiC-Pro)
- [coolpup.py](https://github.com/open2c/coolpuppy)
- [FitHiChIP](https://ay-lab.github.io/FitHiChIP/html/index.html)
- [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)

- Merged `drawTriangleRatioMulti` to `plotHiCfeature`
- Fixed the error "QStandardPaths: XDG_RUNTIME_DIR points to non-existing path '/run/user/1000', please create it with 0700 permissions." when calculating PC1.
- Removed /root/.cpanm/work directory

- Added `libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-render-util0` libraries to avoid an error 'qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.'