Hope you are doing well. I am trying to use this tool on a publically available ".allvalidpairs" file from HiChIP data, my intention is to get a .hic file and a .bedpe file.
The environment is created successfully, then I tried to run it from this step using this code: "$./HiC-Pro/bin/HiC-Pro -i ./hichip/GSM2572593_con_rep1.allvalidPairs.txt -o ./hichip_output -c ./HiC-Pro/config-hicpro.txt -s build_contact_maps"
and it gives me this error message "Error - Installation - config system not detected. Please (re) install HiC-Pro", I checked again the file, and HiCPro doesn't exist in the bin of conda environment, but it exists in the clone folder. Also, I saw this step
"tar -zxvf HiC-Pro-master.tar.gz
cd HiC-Pro-master
Edit config-install.txt file if necessary
make configure
make install"
and I couldn't locate this .tar.gz, sorry it might be a stupid issue since I am a beginner, but can you please lead me in this? and Thanks in advance.
-yussuf
PS: I tried to install it from a standard conda installation using this:
"conda create --name HiCPro python=2.7
conda activate HiCPro
conda install -c davebx hicpro"
The HiCPro file exists in the bin this time, but when i run on my files, it gives me this error
./programs/miniconda3/envs/HiCPro/bin/../scripts//hic.inc.sh: No such file or directory
Dear Nicolas,
Hope you are doing well. I am trying to use this tool on a publically available ".allvalidpairs" file from HiChIP data, my intention is to get a .hic file and a .bedpe file.
So my installation steps were the following:
The environment is created successfully, then I tried to run it from this step using this code: "$./HiC-Pro/bin/HiC-Pro -i ./hichip/GSM2572593_con_rep1.allvalidPairs.txt -o ./hichip_output -c ./HiC-Pro/config-hicpro.txt -s build_contact_maps"
and it gives me this error message "Error - Installation - config system not detected. Please (re) install HiC-Pro", I checked again the file, and HiCPro doesn't exist in the bin of conda environment, but it exists in the clone folder. Also, I saw this step "tar -zxvf HiC-Pro-master.tar.gz cd HiC-Pro-master
Edit config-install.txt file if necessary
make configure make install"
and I couldn't locate this .tar.gz, sorry it might be a stupid issue since I am a beginner, but can you please lead me in this? and Thanks in advance.
-yussuf
PS: I tried to install it from a standard conda installation using this: "conda create --name HiCPro python=2.7 conda activate HiCPro conda install -c davebx hicpro"
The HiCPro file exists in the bin this time, but when i run on my files, it gives me this error ./programs/miniconda3/envs/HiCPro/bin/../scripts//hic.inc.sh: No such file or directory