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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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HiCPro installation error in Ubuntu 20.04 #473

Closed koushik20 closed 3 years ago

koushik20 commented 3 years ago

I am trying to install HiC-Pro in my ubuntu local server and followed the given instructions but when executing make install command I am getting the following error.

(g++ -Wall -O2 -std=c++0x -o build_matrix /home/koushik/Downloads/HiC-Pro_3.1.0/scripts/src/build_matrix.cpp; mv build_matrix /home/koushik/Downloads/HiC-Pro_3.1.0/scripts)
(g++ -Wall -O2 -std=c++0x -o cutsite_trimming /home/koushik/Downloads/HiC-Pro_3.1.0/scripts/src/cutsite_trimming.cpp; mv cutsite_trimming /home/koushik/Downloads/HiC-Pro_3.1.0/scripts)
cp -Ri /home/koushik/Downloads/HiC-Pro_3.1.0 /home/koushik/Downloads/HiC-Pro_3.1.0/HiC-Pro_3.1.0
cp: cannot copy a directory, '/home/koushik/Downloads/HiC-Pro_3.1.0', into itself, '/home/koushik/Downloads/HiC-Pro_3.1.0/HiC-Pro_3.1.0'
make: *** [Makefile:78: cp] Error 1

my config-install file

PREFIX = /home/koushik/Downloads/HiC-Pro_3.1.0
BOWTIE2_PATH = /home/koushik/miniconda3/envs/Hi-ChIP/bin/bowtie2
SAMTOOLS_PATH = /home/koushik/miniconda3/envs/Hi-ChIP/bin/samtools
R_PATH = /usr/bin/R
PYTHON_PATH = /home/koushik/miniconda3/envs/Hi-ChIP/bin/python
CLUSTER_SYS = TORQUE

When run make config every dependency is checked and PATH is in place. Thank you in advance!

nservant commented 3 years ago

Hi, Please try with ;

PREFIX = /home/koushik/Downloads/
BOWTIE2_PATH = /home/koushik/miniconda3/envs/Hi-ChIP/bin/
SAMTOOLS_PATH = /home/koushik/miniconda3/envs/Hi-ChIP/bin/
R_PATH = /usr/bin/
PYTHON_PATH = /home/koushik/miniconda3/envs/Hi-ChIP/bin/
CLUSTER_SYS = TORQUE

and re-run 

make configure
make install
koushik20 commented 3 years ago

Hi,

Thank you for your response. I have followed your suggestions and re-run make install after editing config-install file and got the following message

(g++ -Wall -O2 -std=c++0x -o build_matrix /home/koushik/Downloads/HiC-Pro-master/scripts/src/build_matrix.cpp; mv build_matrix /home/koushik/Downloads/HiC-Pro-master/scripts)
(g++ -Wall -O2 -std=c++0x -o cutsite_trimming /home/koushik/Downloads/HiC-Pro-master/scripts/src/cutsite_trimming.cpp; mv cutsite_trimming /home/koushik/Downloads/HiC-Pro-master/scripts)
cp -Ri /home/koushik/Downloads/HiC-Pro-master /home/koushik/Downloads//HiC-Pro_3.1.0
HiC-Pro installed in /home/koushik/Downloads/HiC-Pro_3.1.0 !

But after I ran HiC-Pro --help it still shows HiC-Pro: command not found

Thank you

nservant commented 3 years ago

Because it is installed in home/koushik/Downloads/HiC-Pro_3.1.0 ! Try to run 

 /home/koushik/Downloads/HiC-Pro_3.1.0/bin/HiC-Pro -h
koushik20 commented 3 years ago

Thank you very much it is running now.