repository does not exist

[lalehan]

Hello, I'm trying to install through git and this error occurs:
fatal: repository 'zhenglz@github.com/zheng/dockingML.git' does not exist

Could you please provide some guidance? Thanks.

[zhenglz]

Hello, I'm trying to install through git and this error occurs:
fatal: repository 'zhenglz@github.com/zheng/dockingML.git' does not exist

Could you please provide some guidance? Thanks.

There is an error in the README.md file. Now the bug has been fixed. The right way to install the package is:

$ cd /home/john/applications
$ pip install networkx
$ pip install mdtraj
$ git clone https://github.com/zhenglz/dockingML.git
$ cd dockingML
$ pip install ./
Or you may use Anaconda to install the package. Please refer to the README page.
$ conda create -name mdanaly python=3.6
$ source activate mdanaly
$ conda install -c omnia mdtraj
$ conda install pandas mpi4py numpy matplotlib sklearn networkx
$ conda install -c rdkit rdkit
$ cd $HOME/applications/dockingML
$ pip install .

[lalehan]

Thank you for the guidance, it actually worked. No problem with installation anymore, however when I run gmx_cmap.py, the error in the picture occurs.

[zhenglz]

Thank you for the guidance, it actually worked. No problem with installation anymore, however when I run gmx_cmap.py, the error in the picture occurs.

I may suggest you have a python 3.5 or 3.6, then install the package. It would be preferred to set up the environment with anaconda.

[lalehan]

I did exactly the same and the error persists:

Does it have anything to do with the default python version on the system?

[zhenglz]

I did exactly the same and the error persists:

Does it have anything to do with the default python version on the system?

Note that although you are using Python 3.5, your python libraries are still 2.7. See the figure you provided.

A potential solution is unset pythonpath using:
$ source deactive # to escape from py35 environment
$ unset PYTHONPATH
$ unset PYTHONHOME
$ source activate py35
$ gmx_cmap.py -h

[lalehan]

Yes, that's what I thought. I wanted to make Python 3 default for that matter, but couldn't do it yet. I tried your solution:

[zhenglz]

Quite strange.

You may now try these:

under py35

$ source activate py35
$ cd dockingML
$ which pip # make sure that pip is in xx/envs/py35/bin/pip
$ pip install ./ # try to install the package again
$ cd xx/dockingML/bin
$ python ./gmx_cmap.py -h

[lalehan]

I think I'll try yum install Glibc 2.14 now and see what happens:

[zhenglz]

The package now is working as desired. But seems some library is not compatible with mdtraj.

Yes, Glibc 2.14 may need to be upgraded.
You may find this link useful:
https://unix.stackexchange.com/questions/176489/how-to-update-glibc-to-2-14-in-centos-6-5

[lalehan]

I was just reading that :)
Thank you very much, really. This was way more than helpful. I'll post here once I manage to run.
Best,

[zhenglz]

I was just reading that :)
Thank you very much, really. This was way more than helpful. I'll post here once I manage to run.
Best,

No problem.

[lalehan]

Looks like my errors get better:

I feel I'm getting somewhat closer. Thanks again!

[zhenglz]

I have never seen such an error. "core dumped" may be caused by a lot of different reasons.
I am not sure how to deal with this error.

But you could try the code in python console and return me your output:
$ python

from mdanaly import cmap
import dockml

[lalehan]

Here it is:

[zhenglz]

Ah, confused.

What about:

python

import mdtraj as mt
import numpy as np