# HiC-Pro安装

## 1.使用conda安装依赖

* python版本为`2.7`

```bash
conda create -n hicpro python=2.7
conda install -y samtools bowtie2 R
```

## 2.安装对应的R包

* 在当前conda环境下运行R
* 也可以绝对路径运行R

```bash
R
install.packages(c('ggplot2','RColorBrewer'))
```

## 3.安装对应的python包

```bash
conda install -y pysam bx-python numpy scipy
```

## 4.配置confir-install.txt安装文件

* `PREFIX`软件安装路径，会在该路径创建一个`HiC-Pro_2.11.1`目录
* `R_PATH`指定conda环境下的R
* `PYTHON_PATH`指定conda环境下的python
* `CLUSTER_SYSCLUSTER_SYS`集群调度系统为`TORQUE,SGE,SLURM,LSF`四个中的一种

```bash
PREFIX = /public/home/yxlong/yxlong/app/
BOWTIE2_PATH = /public/home/yxlong/miniconda3/bin/bowtie2
SAMTOOLS_PATH = /public/home/yxlong/miniconda3/bin/samtools
R_PATH = /public/home/yxlong/miniconda3/envs/hicpro/bin/R
PYTHON_PATH = /public/home/yxlong/miniconda3/envs/hicpro/bin/python
CLUSTER_SYS = LSF
```


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://zpliu.gitbook.io/booknote/sheng-xin-ruan-jian/hicpro-an-zhuang.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.