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kundajelab / dragonn

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
http://kundajelab.github.io/dragonn/
MIT License
257 stars 71 forks source link

Python setup.py installation issue for bleeding edge dragonn #37

Closed rodriguesk closed 7 years ago

rodriguesk commented 7 years ago

Hi,

I git cloned the dragonn repo in a clean virtual environment and ran "pip install --editable dragonn/", and received the following dependency error:

(dragonn) [kameronr@sh-112-07 ~]$ pip install --editable dragonn/ Obtaining file:///home/users/kameronr/dragonn Requirement already satisfied: numpy>=1.9 in ./anaconda2_correct/envs/dragonn/lib/python2.7/site-packages (from dragonn==0.1.3) Requirement already satisfied: keras==0.3.3 in ./anaconda2_correct/envs/dragonn/lib/python2.7/site-packages (from dragonn==0.1.3) Collecting deeplift==0.5.1-theano (from dragonn==0.1.3) Could not find a version that satisfies the requirement deeplift==0.5.1-theano (from dragonn==0.1.3) (from versions: ) No matching distribution found for deeplift==0.5.1-theano (from dragonn==0.1.3)

Running "python setup.py install" gives a bunch of issues too; the command ends with:

In file included from /lscratch/kameronr/easy_install-hE1SBn/h5py-2.7.0/h5py/defs.c:515:0: /lscratch/kameronr/easy_install-hE1SBn/h5py-2.7.0/h5py/api_compat.h:27:18: fatal error: hdf5.h: No such file or directory

include "hdf5.h"

^ compilation terminated.

Would be great to hear about a fix for this. Thanks!

jisraeli commented 7 years ago

Your error trace for python setup.py install complains about missing files for h5py. Could you try installing h5py with conda install h5py?

jisraeli commented 7 years ago

Closing the issue due to lack of activity. Feel free to reopen if there is follow up.