Question: Problems in HiC pro installation/Finding libraries in Python
gravatar for ra2967
7 months ago by
ra296720 wrote:

Hello all,

I am a postdoc in Columbia University trying to install HiC pro. I dowloaded and installed all the dependencies, but when I try to run the install command 'make configure' in the folder where I unzipped the HiC pro pipeline, I obtained this message:

export /Users/Robert/anaconda3/bin/bowtie2 in PATH export /usr/local/bin/samtools in PATH export /usr/local/bin/R in PATH Checking dependencies ... Checking Python libraries ... Traceback (most recent call last): File "../scripts/install/", line 25, in <module> if vcmp(bx.__version__, '0.5.0') == -1: File "../scripts/install/", line 19, in vcmp return cmp(normalize(version1), normalize(version2)) NameError: name 'cmp' is not defined Can not proceed without the required Python libraries, please install them and re-run

However, if I Install bx-python, this is the message: pip install bx-python Requirement already satisfied: bx-python in /usr/local/lib/python3.7/site-packages (0.8.4) Requirement already satisfied: six in /usr/local/lib/python3.7/site-packages (from bx-python) (1.12.0) Requirement already satisfied: numpy in /usr/local/lib/python3.7/site-packages (from bx-python) (1.16.4)

So it seems that I have already it installed. Can you help me? May it be that it is installed, but the pipeline is not finding it? I know that many people have had problems to install this pipeline, but I see that they had different problems...

Thanks, Robert

libraries hic hicpro python • 281 views
ADD COMMENTlink written 7 months ago by ra296720
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1510 users visited in the last hour