BjornFJohansson / pydna

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
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pypandoc error during install with pip #33

Closed mcrone closed 7 years ago

mcrone commented 7 years ago

Just wanted to make sure I'm not missing something obvious. I'm trying to install pydna on Oracle Linux and I get this error: RuntimeError: Format missing, but need one (identified source as text as no file with that name was found).

It's a pypandoc error. Any help on how to get past this would be awesome!

Thanks!

BjornFJohansson commented 7 years ago

Hi, which version are you trying to install? Are you using Anaconda or system Python? There might be a dependency missing. Could you paste the entire traceback here, please.

mcrone commented 7 years ago

I'm just using the system python and just using sudo pip install pydna

This is the traceback: Collecting pydna Using cached pydna-1.1.5.tar.gz Complete output from command python setup.py egg_info: Traceback (most recent call last): File "", line 1, in File "/tmp/pip-build-jt61RH/pydna/setup.py", line 32, in long_description=read_md('README.md'), File "/tmp/pip-build-jt61RH/pydna/setup.py", line 14, in read_md = lambda f: convert(f, 'rst') File "/usr/lib/python2.7/site-packages/pypandoc/init.py", line 66, in convert raise RuntimeError("Format missing, but need one (identified source as text as no " RuntimeError: Format missing, but need one (identified source as text as no file with that name was found). Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-jt61RH/pydna/

BjornFJohansson commented 7 years ago

I see, first problem is that you have python 2.7, while pydna now only works with python 3. perhaps if you use pip3 instead of pip? or have a look at this: http://stackoverflow.com/questions/29712519/how-do-i-use-pip-3-with-python-3-4

Some dependencies like numpy etc will not be installed automatically. Have you tried Anaconda? Is solves many of these problems.

mcrone commented 7 years ago

Thanks for the help. I'll just try anaconda. I had previously had a bad experience with anaconda messing with my system python and that was why I was trying to avoid it (although that was under OSX).