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"description": "\n# hictools\n\nhictools is a collection of handful tools for processing hic data based on:\n\n- `nextflow` [1](#1) `pairtools` [2](#2) `cooler` [3](#3) `higlass` [4](#4) `......`\n\nCurrently, hictools is mainly composed of 3 parts:\n\n- A `nextflow` based hic-data processing `pipeline`.\n- Python `api` for handling outputs of the pipeline(`.cool`).\n- A simple yet user friendly `higlass server`.\n\n# requirements\n\n- [python3.6+](https://www.python.org/downloads/)\n- [nextflow](https://www.nextflow.io/)\n\n# Install\n\n```\npip install hictoools\n```\n\n# Usage\n\n## Pipeline\n\n- ##### Fill in the config file and run.\n\n Fill in a config file in order to specify the desired sample files(.fastq) to process.\nYou can find a template config file in the current folder named `config_template.yml` after you executed this command:\n\n```bash\nnextflow pull zhqu1148980644/hictools && nextflow run zhqu1148980644/hictools\n```\n\n- ##### Run the pipeline with this config file.\n\n```bash\nnextflow run -params-file config_template.yml hictools -resume \\\n-profile standard\n# Choose the cluster profile if you wish to run in a another executor(platform) by using:\n# -profile cluster\n```\n\n- ##### Outputs\n\nYou can find output folders after the execution of pipeline finished in the same directory as the current config file.\n\n```bash\nwork/ # Working directory generated by nextflow.\nlog/ # Logging file generated by nextflow.\nresults/ # Main folder containing results of this pipeline.\n fastqc/ bams/ pairs/ cools/ features/ other/\n```\n\n***\n\n## Visualize\n\n- ##### Start a api server to provide tilesets\n\nFiles added into this folder will be automatically recorded and converted using `clodius`.\n\ne.g. `.mcool` `.bam` `.bigwig` `.bed` ....\n\n```bash\nhictools hgserver serve --workers 10 --paths ./\n>>\nOpenning api server: http://x.x.x.x:48005/api/v1\nTilesets Database: sqlite:////store/qzhong/.hictools_hgserver.db\nRun 'hictools hgserver view --api_port 48005 to visualize in your web browser.\n```\n\n- ##### Start higlass web app and visit in browser\n\n```bash\nhictools hgserver view --api_port 48405\n>>\nGo visit http://x.x.x.x:8888 in browser.\n```\n\n***\n\n## CLI\n\n***\n\n## API\n\nCheck source codes for details.\n\n---\n\n## Notes\n\n> `nextflow` is a pipeline framework based on the dataflow programing model, which can be spectacularly expressive when writing complex distributed pipelines.\n\n> Pipeline built by `Nextflow` can be executed in multi platforms including SGE, LSF, SLURM, PBS, HTCondor batch schedulers , Kubernetes and Amazon AWS cloud platform by changing the executor specified in `~/.nextflow/assets/zhqu1148980644/hictools/nextflow.config`. The default executor is `SGE`(Sun Grid Engine). You may need to change it depending on the platform you use.\n\n> The pipeline procesures in hictools are similar to that of the `Hi-C Processing Pipeline` used by `4DN`.\n\n ## Reference\n\n- [nextflow](https://github.com/nextflow-io/nextflow \"nextflow\") A DSL for data-driven computational pipelines. \n\n- [pairtools](https://github.com/mirnylab/cooler \"pairtools\") A cool place to store your Hi-C. \n\n- [cooler](https://github.com/mirnylab/pairtools \"cooler\") CLI tools to process mapped Hi-C data. \n\n- [higlass](https://github.com/higlass/higlass \"higlass\") Fast large scale matrix visualization for the web. \n\n\n",
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