Question: I can't install HiC-Pro
0
gravatar for rahman.samir33
4 months ago by
rahman.samir330 wrote:

Hi everyone, my name is Samir. I am a postdoc at Mount Sinai. I am very new to genomics and computational biology. I am trying to install HiC Pro, but having difficulty doing so. I downloaded the HiC-Pro-2.10.0.tar.gz file and unzipped it. I ran the following code in the terminal as suggested and received an error.

tar -zxvf HiC-Pro-2.10.0.tar.gz

tar: Error opening archive: Failed to open 'HiC-Pro-2.10.0.tar.gz'

I installed all the dependencies via homebrew, and I have edited the config-install.txt file as shown below:

PREFIX = /usr/local/Cellar
BOWTIE2_PATH = /usr/local/Cellar/bowtie2/2.3.4
SAMTOOLS_PATH = /usr/local/Cellar/samtools/1.7
R_PATH = /usr/local/Cellar/r/3.4.3_1
PYTHON_PATH = /usr/local/Cellar/python/2.7.14_2
CLUSTER_SYS = SLURM

I would really appreciate your help. Thanks.

ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 4 months ago by rahman.samir330

If that file is indeed in the same directory where you are running this from then you may have a corrupt file. What happens if you try tar -zxvf ./HiC-Pro-2.10.0.tar.gz

ADD REPLYlink written 4 months ago by genomax49k

the error has nothing to do with HiC Pro, try to cd into directory of HiC-Pro before run tar -zxvf HiC-Pro-2.10.0.tar.gz

ADD REPLYlink written 4 months ago by Chen670

Hi, thanks for your replies. I realized I was in the wrong directory, and have actually advanced a bit. Here is the error message I receive now:

Starting HiC-Pro installation ...

export /usr/local/Cellar/bowtie2/2.3.4 in PATH

export /usr/local/Cellar/samtools/1.7 in PATH

export /usr/local/Cellar/r/3.4.3_1 in PATH

export /usr/local/Cellar/python/2.7.14_2 in PATH

Checking dependencies ... 

Checking Python libraries ...

Traceback (most recent call last):

  File "../scripts/install/check_pythonlib.py", line 28, in <module>

    raise ImportError('Error - bx-python cannot be imported')  

ImportError: Error - bx-python cannot be imported


Can not proceed without the required Python libraries, please install them and re-run

I have downloaded bx-python-master.zip and unzipped it. How and where do I install bx-python?

ADD REPLYlink modified 4 months ago by genomax49k • written 4 months ago by rahman.samir330

You should install using the pip or conda method described on bx-python page.

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized.

ADD REPLYlink written 4 months ago by genomax49k

When I run "pip install bx-python", I get this message:

Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/fq/hmbm61rx6bv9kpqhrjyycd9h0000gn/T/pip-build-aFTaS0/bx-python/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/fq/hmbm61rx6bv9kpqhrjyycd9h0000gn/T/pip-d1ijEl-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/fq/hmbm61rx6bv9kpqhrjyycd9h0000gn/T/pip-build-aFTaS0/bx-python/

When I run conda install -c bioconda bx-python, I get this message:

-bash: conda: command not found
ADD REPLYlink modified 4 months ago by genomax49k • written 4 months ago by rahman.samir330

What OS are you installing on? Is this your personal machine or a shared cluster/server? If latter then you may want to work with the sys admins to see if they can install this software for you.

ADD REPLYlink written 4 months ago by genomax49k

MacOS. This is my laptop.

ADD REPLYlink written 4 months ago by rahman.samir330

You can install conda or pip for macOS in that case.

ADD REPLYlink written 4 months ago by genomax49k

Hey, thank you so much! I dowloaded Anaconda and was able to install the missing Python libraries. This is the message I receive now:

Starting HiC-Pro installation ...
export /usr/local/Cellar/bowtie2/2.3.4 in PATH
export /usr/local/Cellar/samtools/1.7 in PATH
export /usr/local/Cellar/r/3.4.3_1 in PATH
export /usr/local/Cellar/python/2.7.14_2 in PATH
Checking dependencies ... 
Checking Python libraries ...
The required Python libraries appear to be already installed. 
Checking R installation ...
Installing missing R packages ...
R packages appear to be installed successfully
Bowtie2 Aligner appears to be already installed. 
Samtools appears to be already installed. 
Dependencies checked !
Check HiC-Pro configuration ... 
Configuration for SLURM system.

I then ran "make install", and HiC-Pro was installed. :D

ADD REPLYlink modified 4 months ago by genomax49k • written 4 months ago by rahman.samir330
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