HiCExplorer v2.0 installation error

[CMylonas]

Installed v2.0 via pip install git+https://github.com/deeptools/HiCExplorer@2.0.1-bugfix

I get the following error every time I run any of the commands. The 1.8v seems to be running smoothly.

Traceback (most recent call last): File "/beegfs/group_pt/home/CMylonas/.Python/2.7/bin/hicFindTADs", line 4, in from hicexplorer.hicFindTADs import main File "/beegfs/group_pt/home/CMylonas/.Python/2.7/lib/python2.7/site-packages/hicexplorer/hicFindTADs.py", line 9, in from hicexplorer import HiCMatrix as hm File "/beegfs/group_pt/home/CMylonas/.Python/2.7/lib/python2.7/site-packages/hicexplorer/HiCMatrix.py", line 20, in import cooler File "/beegfs/group_pt/home/CMylonas/.Python/2.7/lib/python2.7/site-packages/cooler/init.py", line 32, in from .api import Cooler, get, info, chroms, bins, pixels, matrix, annotate File "/beegfs/group_pt/home/CMylonas/.Python/2.7/lib/python2.7/site-packages/cooler/api.py", line 10, in import h5py File "build/bdist.linux-x86_64/egg/h5py/init.py", line 10, in File "build/bdist.linux-x86_64/egg/h5py/_errors.py", line 7, in File "build/bdist.linux-x86_64/egg/h5py/_errors.py", line 6, in bootstrap ImportError: libhdf5.so.9: cannot open shared object file: No such file or directory

[bgruening]

Can you check if you have libhdf5 installed on your system? If not could you use conda as packages manager and try a conda create -n hicexplorer hicexplorer -c bioconda?

[joachimwolff]

Thanks a lot for using HiCExplorer. I saw that you are new on github, therefore I want to clarify that the recommended stable version is always the in master branch. This release is available per conda as @bgruening already mentioned and is the recommended way to install the HiCExplorer. In non-master branches we develop new features or as it is with the 2.0.1-bugfix branch, collect bug fixes for a next release. This means that the 2.0.1-bugfix branch is not declared as stable and should only be used if you know what you do. Anyway, I appreciate it that someone is testing the bugfix branch, this helps a lot to detect errors in an early stage. It looks like you are missing dependencies. The dependencies are listed in the requirements.txt file, for Python 2.7 you need to add the dependency configparser. To fix you issue: pip install -r requirements.txt && pip install configparser The requirements.txt file you can find here: https://github.com/deeptools/HiCExplorer/blob/master/requirements.txt

Please let me know if I this is solving your issue or if you need additional help.

[fidelram]

I suggested @CMylonas to put the issue here as they are interested on running hicPCA which is not yet part of the master branch.

[joachimwolff]

@fidelram hicPCA is part of the 2.0 release. Or do you mean specific bug fixes in 2.0.1?

[fidelram]

The original message I got before moving to github was:

... hicPCA is only available in v2.0 which is not available through "pip".
I downloaded it directly from github but I'm getting the following error:

File "build/bdist.linux-x86_64/egg/h5py/__init__.py", line 10, in <module>
  File "build/bdist.linux-x86_64/egg/h5py/_errors.py", line 7, in <module>
  File "build/bdist.linux-x86_64/egg/h5py/_errors.py", line 6, in __bootstrap__
ImportError: libhdf5.so.9: cannot open shared object file: No such file or directory

Thus I suggested the bugfix branch. But the problem seems to be cooler and hdf5 version in either case.

One option is to start a new environment with conda and install a fresh copy of cooler.

[fidelram]

@CMylonas How did you installed cooler?

If you installed it using conda (or the conda version of HiCExplorer) this may help: I had a similar hdf5 issue recently. I searched which version of hdf5 was used for the conda package I needed and then installed that hdf5 version.

[CMylonas]

@fidelram I had a problem installing some dependencies with conda. The core facility installed v2.0 for me through conda and now it works fine

Thank you for all the suggestions

[joachimwolff]

@CMylonas Good to hear that it works now. @fidelram Does this mean we have to manage the dependencies with pip better? I just try to understand what went wrong and how we can improve based on this.

[fidelram]

I don't know if this is related with pip or with conda or both. @CMylonas, in case we have a similar issue in the future, can you tell us how did you first installed HiCExplorer? To update you used pip and that is when you got the error right?

[CMylonas]

@fidelram Exactly! pip install caused the error whereas with conda it runs smoothly

[joachimwolff]

I tried to reproduce it in a new conda environment and failed. I was using the command pip install git+https://github.com/deeptools/HiCExplorer@2.0.1-bugfix. If I run any command e.g. hicBuildMatrix --help it runs without an error.