Issue installing HiC-Pro_3.0.0

[Dilan Soriano Rosales]

Hi, I am Eric from Mexico City and I am trying to install HiC-Pro version 3.0.0. 

What I did first was to clone the git repository in which HiC-Pro is contained. Then created a new environment with the .yml file included in the repository, activated such environment and edited the config-install file with my respective dependencies paths. The problem is that when I try to install HiC-Pro, seems to not recognize my python path. I already made sure that the python version is 3.7.6 as indicated in the .yml file, and also checked the python path with 'which'.

Here I add the commands used:

 

git clone https://github.com/nservant/HiC-Pro.git

conda env create -f /home/jarvis/Documents/Dilan/HiC-Pro/environment.yml 

conda activate HiC-Pro_v3.0.0/ 

make configure install

make -f ./scripts/install/Makefile CONFIG_SYS=./config-install.txt

make[1]: Entering directory '/home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/HiC-Pro'

./scripts/install/install_dependencies.sh -c ./config-install.txt -p /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/ -o /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin//HiC-Pro_3.0.0 -q

Make sure internet connection works for your shell prompt under current user's privilege ...

Starting HiC-Pro installation ...

export /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/bowtie2 in PATH

export /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/samtools in PATH

export /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/R in PATH

export /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/python in PATH

Can not proceed without Python, please install and re-run

make[1]: *** [scripts/install/Makefile:41: configure] Error 1

make[1]: Leaving directory '/home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/HiC-Pro'

make: *** [Makefile:40: configure] Error 2

#########################################################

#environment.yml

#########################################################

#   conda env create -f environment.yml

name: HiC-Pro_v3.0.0

channels:

  - conda-forge

  - bioconda

  - defaults

dependencies:

  - python=3.7.6

  - scipy=0.15.1

  - numpy=1.8.2

  - iced=0.5.4

  - bx-python=0.5.0

  - pysam=0.8.3

  - cooler=0.8.6

  - r-base=3.6.3

  - r-ggplot2=2.2.1

  - r-rcolorbrewer=1.1_2

  - r-gridbase=0.4_7

  - bowtie2=2.3.5

  - samtools=1.9

  - multiqc=1.8

###############################################################

#config-install.txt

#########################################################################

## Paths and Settings  - Start editing here !

#########################################################################

PREFIX = /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/

BOWTIE2_PATH = /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/bowtie2

SAMTOOLS_PATH = /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/samtools

R_PATH = /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/R

PYTHON_PATH =/home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/python 

CLUSTER_SYS =

[nservant]

Hi,

You should not provide the binary in the path ... could you try ;

```

PREFIX = /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/

BOWTIE2_PATH = /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/

SAMTOOLS_PATH = /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/

R_PATH = /home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/

PYTHON_PATH =/home/jarvis/anaconda3/envs/HiC-Pro_v3.0.0/bin/

```

Thanks