Trouble installing HiC-Pro
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7 weeks ago
Amina • 0

Hello,

I am trying to install HiC-Pro on a slurm cluster but I am getting errors. I downloaded the Hi-C Pro repository to my system and created the HiC-Pro_v3.1.0 environment from the environment.yml file. I then ran the commands "make configure" and "make install". I updated the config-install.txt as such:

PREFIX = /data/homezvol2/aminaoh/.conda/envs/HiC-Pro_v3.1.0

BOWTIE2_PATH = /opt/rcic/Modules/modulefiles/BIOTOOLS/bowtie2/2.4.4

SAMTOOLS_PATH = /opt/rcic/Modules/modulefiles/BIOTOOLS/samtools/1.10

R_PATH = /opt/rcic/Modules/modulefiles/LANGUAGES/R/4.0.4

PYTHON_PATH = /opt/rcic/Modules/modulefiles/LANGUAGES/python/3.8.0

CLUSTER_SYS = SLURM


However, whenever I try to run the software, I get this error:

/export/spool/slurm/slurmd.spool/job8313018/slurm_script: line 11: HiC-Pro: command not found


Has anyone ran into this issue? I am not sure how to fix it and would appreciate any help.

hic-pro hic hicpro • 486 views
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Installation of the software and running it are two different things. I assume you have successfully installed the software? If you have then it may be a matter of making sure that the \$PATH includes the location where you installed the HiC-Pro program.

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Hello GenoMax,

Thank you for your response. I assumed there was something wrong with the installation if the command was not found, but maybe I am not moving to the right path. When I submit the script to run the software, I move to the location where I downloaded the program like this:

cd /dfs3b/mbt/aminaoh/hic-pro
HiC-Pro -i /dfs3b/mbt/aminaoh/Xenopus_HiC_Niu -o hic_test -c /dfs3b/mbt/aminaoh/HiC-Pro/config-hicpro.txt

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Entering edit mode

You may need to type ./HiC-Pro to specify that the program is in your current directory. Or you can use the whole path:

/dfs3b/mbt/aminaoh/hic-pro/HiC-Pro

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Hello Mensur,

Using the whole path solved the issue. Thank you :)