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biocore / American-Gut

American Gut open-access data and IPython notebooks
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conda_req and pip_req differences #203

Closed iugrina closed 8 years ago

iugrina commented 8 years ago

Hi,

I'm trying to install americangut and I've stumbled upon some (to me) interesting/strange things. Is there a reason why pip_requirements.txt and conda_requirements.txt differ (e.g. one contains qiime while other doesn't, cython, IPython, pandas, ...).

wasade commented 8 years ago

The intention is for them to be used together (see .travis.yml). Basically, some of the reqs are not available in conda. The preference for conda over pip is that it is much more reliable than pip especially for scipy and matplotlib.

iugrina commented 8 years ago

However, if one doesn't use conda he will have problems with installing ag. You should maybe write an INSTALL.md to explain the bootstraping in more details.

wasade commented 8 years ago

It's not feasible to support everyones specific environment and our intention is to support the general case on Linux and OSX. conda is not a requirement itself, but it greatly simplifies setup of the environment, and is a standard in the scientific python community. In fact, I think everything in the pip list has at this point migrated to conda. That being said, I do agree that having an INSTALL.md would be useful to include in the repository. We would also be excited for a pull request that would expand pip support if you're interested in contributing.

On Wed, Mar 9, 2016 at 11:28 AM, Ivo Ugrina notifications@github.com wrote:

However, if one doesn't use conda he will have problems with installing ag. You should maybe write an INSTALL.md to explain the bootstraping in more details.

— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/issues/203#issuecomment-194466509 .

iugrina commented 8 years ago

Just to be clear, I completely understand that it is not possible to satisfy everyones wishes and I really value the time and effort you've included in making this free and open :+1:

As for the pip, I'm working on INSTALL.md for Debian 8 (bare), pip, virtenv ;) You'll get the pull request soon I hope :)

wasade commented 8 years ago

Ah, that's fantastic! Looking forward to it, and thank you for prodding the code :)

iugrina commented 8 years ago

Resolved with commit #211