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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Can't Install HiC-Pro #393

Closed Jacobvazquez18 closed 3 years ago

Jacobvazquez18 commented 3 years ago

Hello, after installing all the necessary libraries, I am getting an error when I enter the "make configure" command. It is shown below:

Starting HiC-Pro installation ... Checking dependencies ... Checking Python libraries ... /home/helix2/miniconda3/lib/python3.8/site-packages/iced/normalization/_ca_utils.py:8: UserWarning: The API of this module is likely to change. Use only for testing purposes warnings.warn( The required Python libraries appear to be already installed. Checking R installation ... The required R packages appear to be already installed. Bowtie2 Aligner appears to be already installed. Samtools appears to be already installed. Dependencies checked ! Check HiC-Pro configuration ... Warning : Scheduler system not defined - Default is Torque/PBS Configuration for TORQUE/PBS system.

make[1]: Leaving directory '/home/helix2/Downloads/HiC-Pro-3.0.0'

Do you know how to avoid this? It's stopping me from installing HiC Pro

nservant commented 3 years ago

Hi, I do not see any error message ? Did you run make install after the 'configure ?

Jacobvazquez18 commented 3 years ago

Yes, after I run "make install" I get the following output:

make install (g++ -Wall -O2 -std=c++0x -o build_matrix /home/helix2/Downloads/HiC-Pro-3.0.0/scripts/src/build_matrix.cpp; mv build_matrix /home/helix2/Downloads/HiC-Pro-3.0.0/scripts) (g++ -Wall -O2 -std=c++0x -o cutsite_trimming /home/helix2/Downloads/HiC-Pro-3.0.0/scripts/src/cutsite_trimming.cpp; mv cutsite_trimming /home/helix2/Downloads/HiC-Pro-3.0.0/scripts) cp -Ri /home/helix2/Downloads/HiC-Pro-3.0.0 /usr/local/bin//HiC-Pro_3.0.0 cp: cannot create directory '/usr/local/bin//HiC-Pro_3.0.0': Permission denied make: *** [Makefile:78: cp] Error 1

nservant commented 3 years ago

you do not have the rigths to install HiC-Pro in /usr/local/bin Update the PREFIX= in the config-install.txt file before running the installation

Jacobvazquez18 commented 3 years ago

Ok so I updated the PREFIX= and did "make configure" and then "make install" and I'm asked if I want to overwrite all of the files one by one?

make install (g++ -Wall -O2 -std=c++0x -o build_matrix /home/helix2/Downloads/HiC-Pro/scripts/src/build_matrix.cpp; mv build_matrix /home/helix2/Downloads/HiC-Pro/scripts) (g++ -Wall -O2 -std=c++0x -o cutsite_trimming /home/helix2/Downloads/HiC-Pro/scripts/src/cutsite_trimming.cpp; mv cutsite_trimming /home/helix2/Downloads/HiC-Pro/scripts) cp -Ri /home/helix2/Downloads/HiC-Pro /home/helix2/Downloads/HiC-Pro/HiC-Pro_3.0.0 cp: overwrite '/home/helix2/Downloads/HiC-Pro/HiC-Pro_3.0.0/HiC-Pro/.gitignore'?

Jacobvazquez18 commented 3 years ago

Now after saying it was downloaded in a folder called HiC-Pro_3.0.0, it's saying I need to re install it when I enter "HiC-Pro --help". Here's the output:

HiC-Pro --help usage : HiC-Pro -i INPUT -o OUTPUT -c CONFIG [-s ANALYSIS_STEP] [-p] [-h] [-v] Use option -h|--help for more information Error - Installation - config system not detected. Please (re) install HiC-Pro !

nservant commented 3 years ago 
cp -Ri /home/helix2/Downloads/HiC-Pro /home/helix2/Downloads/HiC-Pro/HiC-Pro_3.0.0
cp: overwrite '/home/helix2/Downloads/HiC-Pro/HiC-Pro_3.0.0/HiC-Pro/.gitignore'?

You cannot install it in the path where you have downloaded it ! Please set another prefix. Note that it will create the HiC-Pro_3.0.0 folder by itself