install successful

(hic-seq) 16:31:03 jiarongf@172.16.10.223:/data1/jiarongf/HGPS_Hic_seq/hic-pro/HiC-Pro-3.1.0
$
make configure
make -f ./scripts/install/Makefile CONFIG_SYS=./config-install.txt
make[1]: Entering directory '/data1/jiarongf/HGPS_Hic_seq/hic-pro/HiC-Pro-3.1.0'
./scripts/install/install_dependencies.sh -c ./config-install.txt -p /usr/local/bin/ -o /usr/local/bin//HiC-Pro_3.1.0 -q
Make sure internet connection works for your shell prompt under current user's privilege ...
Starting HiC-Pro installation !
Checking dependencies
- Python libraries ...OK
- R installation ...OK
- Bowtie2 installation ...OK
- Samtools installation ...OK

Checking HiC-Pro configuration
- Configuration for TORQUE/PBS system ...OK

done !
make[1]: Leaving directory '/data1/jiarongf/HGPS_Hic_seq/hic-pro/HiC-Pro-3.1.0'

process

1.conda create env

conda env list #obtain conda env
conda create  -n hic-seq python=3.8.8
#此处必须是大于3.7的版本
mkdir hic-pro
cd hic-pro/
wget https://github.com/nservant/HiC-Pro/archive/refs/tags/v3.1.0.tar.gz
l
tar -zxvf v3.1.0.tar.gz
conda install -c bioconda bx-python
conda install -c ipyrad pysam
conda install -c conda-forge numpy
conda install -c conda-forge scipy
conda install -c bioconda iced
#如果不安装上面的包直接make configure 会报错python没有依赖包
conda install bowtie2
#这里一定记得给自己目前的环境安装bowtie2
bowtie2

接着修改install文件

#config-install.txt

#########################################################################
## Paths and Settings  - Start editing here !
#########################################################################

PREFIX = /data1/jiarongf/HGPS_Hic_seq/hic-pro/
BOWTIE2_PATH = /data1/jiarongf/anaconda3/envs/hic-seq/bin/bowtie2
SAMTOOLS_PATH = /data/anaconda3/bin/samtools
R_PATH = /usr/bin/R
PYTHON_PATH = /data1/jiarongf/anaconda3/envs/hic-seq/bin/python
CLUSTER_SYS = TORQUE

这里哪个软件不知道位置直接which就好了
第一个文件夹的位置我是

(hic-seq) 16:43:37 jiarongf@172.16.10.223:/data1/jiarongf/HGPS_Hic_seq/hic-pro
$
l
HiC-Pro_3.1.0/  HiC-Pro-3.1.0/  v3.1.0.tar.gz

其实就是下载hicpro的位置
接下来接着安装

(hic-seq) 16:42:08 jiarongf@172.16.10.223:/data1/jiarongf/HGPS_Hic_seq/hic-pro/HiC-Pro-3.1.0
$
make configure
make -f ./scripts/install/Makefile CONFIG_SYS=./config-install.txt
make[1]: Entering directory '/data1/jiarongf/HGPS_Hic_seq/hic-pro/HiC-Pro-3.1.0'
./scripts/install/install_dependencies.sh -c ./config-install.txt -p /data1/jiarongf/HGPS_Hic_seq/hic-pro/ -o /data1/jiarongf/HGPS_Hic_seq/hic-pro//HiC-Pro_3.1.0 -q
Make sure internet connection works for your shell prompt under current user's privilege ...
Starting HiC-Pro installation !
export /data1/jiarongf/anaconda3/envs/hic-seq/bin/bowtie2 in PATH
export /data/anaconda3/bin/samtools in PATH
export /usr/bin/R in PATH
export /data1/jiarongf/anaconda3/envs/hic-seq/bin/python in PATH
Checking dependencies
- Python libraries ...OK
- R installation ...OK
- Bowtie2 installation ...OK
- Samtools installation ...OK

Checking HiC-Pro configuration
- Configuration for TORQUE/PBS system ...OK

done !
make[1]: Leaving directory '/data1/jiarongf/HGPS_Hic_seq/hic-pro/HiC-Pro-3.1.0'
(hic-seq) 16:42:26 jiarongf@172.16.10.223:/data1/jiarongf/HGPS_Hic_seq/hic-pro/HiC-Pro-3.1.0
$
make install
(g++ -Wall -O2 -std=c++0x -o build_matrix /data1/jiarongf/HGPS_Hic_seq/hic-pro/HiC-Pro-3.1.0/scripts/src/build_matrix.cpp; mv build_matrix /data1/jiarongf/HGPS_Hic_seq/hic-pro/HiC-Pro-3.1.0/scripts)
(g++ -Wall -O2 -std=c++0x -o cutsite_trimming /data1/jiarongf/HGPS_Hic_seq/hic-pro/HiC-Pro-3.1.0/scripts/src/cutsite_trimming.cpp; mv cutsite_trimming /data1/jiarongf/HGPS_Hic_seq/hic-pro/HiC-Pro-3.1.0/scripts)
cp -Ri /data1/jiarongf/HGPS_Hic_seq/hic-pro/HiC-Pro-3.1.0 /data1/jiarongf/HGPS_Hic_seq/hic-pro//HiC-Pro_3.1.0
HiC-Pro installed in /data1/jiarongf/HGPS_Hic_seq/hic-pro/HiC-Pro_3.1.0 !

其实上述只有两个命令

make configure
make install

如果自己不是sudo的话记得更改config-install文件，不然第一个文件夹的位置会在别的目录，自己并没有权限去创建文件夹