Trouble installing Hic-Pro v3.1.0

[Ruchi-281]

I used conda to install hic-pro. The installation was successful but still hic-pro is not recognized. I used the below commands:

$conda env create -f environment.yml -p hic_pro $conda activate /media/dasdata3/ruchi/HiC-Pro/hic_pro

configuration file

PREFIX = /media/dasdata3/ruchi/HiC-Pro/ BOWTIE2_PATH = /media/dasdata3/ruchi/HiC-Pro/hic_pro/bin/ SAMTOOLS_PATH = /media/dasdata3/ruchi/HiC-Pro/hic_pro/bin/ R_PATH = /media/dasdata3/ruchi/HiC-Pro/hic_pro/bin/ PYTHON_PATH = /media/dasdata3/ruchi/HiC-Pro/hic_pro/bin/ CLUSTER_SYS = TORQUE

$make configure make -f ./scripts/install/Makefile CONFIG_SYS=./config-install.txt make[1]: Entering directory '/media/dasdata3/ruchi/HiC-Pro' /media/dasdata3/ruchi/HiC-Pro/scripts/install/install_dependencies.sh -c ./config-install.txt -p /media/dasdata3/ruchi/HiC-Pro/ -o /media/dasdata3/ruchi/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 /media/dasdata3/ruchi/HiC-Pro/hic_pro/bin/ in PATH export /media/dasdata3/ruchi/HiC-Pro/hic_pro/bin/ in PATH export /media/dasdata3/ruchi/HiC-Pro/hic_pro/bin/ in PATH export /media/dasdata3/ruchi/HiC-Pro/hic_pro/bin/ 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 '/media/dasdata3/ruchi/HiC-Pro' $make install (g++ -Wall -O2 -std=c++0x -o build_matrix /media/dasdata3/ruchi/HiC-Pro/scripts/src/build_matrix.cpp; mv build_matrix /media/dasdata3/ruchi/HiC-Pro/scripts) (g++ -Wall -O2 -std=c++0x -o cutsite_trimming /media/dasdata3/ruchi/HiC-Pro/scripts/src/cutsite_trimming.cpp; mv cutsite_trimming /media/dasdata3/ruchi/HiC-Pro/scripts) HiC-Pro installed in /media/dasdata3/ruchi/HiC-Pro ! $HiC-Pro --help HiC-Pro: command not found

[ZhaoRanze]

maybe... PATH was needed. like this: PATH/bin/HiC-Pro -h

[nservant]

Sorry for the late reply. Indeed, you just need to add /media/dasdata3/ruchi/HiC-Pro/bin in your PATH or to run /media/dasdata3/ruchi/HiC-Pro/bin/HiC-Pro --help best